[gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
commit: 7f9384c065b99e3a858415a8a838438d9f70bcdf Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue May 2 12:08:24 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue May 2 12:15:10 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7f9384c0 sci-biology/khmer: treeclean Signed-off-by: Andrew Ammerlaan 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..0 --- 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[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest - -python_prepare_all() { - # do not depend on pytest-runner - sed -i "/pytest-runner/d" setup.py || die - distutils-r1_python_prepare_all -} diff --git a/sci-biology/khmer/metadata.xml b/sci-biology/khmer/metadata.xml deleted file mode 100644 index 91ed395d8..0 --- a/sci-biology/khmer/metadata.xml +++ /dev/null @@ -1,16 +0,0 @@ - -http://www.gentoo.org/dtd/metadata.dtd;> - - - mmokr...@fold.natur.cuni.cz - Martin Mokrejs - - - sci-biol...@gentoo.org - Gentoo Biology Project - - - ged-lab/khmer - khmer - -
[gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
commit: d7637214cd6c37456262bc62ff07eab1b1dae6b3 Author: Andrew Ammerlaan riseup net> AuthorDate: Wed Dec 30 18:39:36 2020 + Commit: Aisha Tammy aisha cc> CommitDate: Wed Dec 30 19:02:35 2020 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d7637214 sci-biology/khmer: version bump 2.1.1 Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> Closes: https://github.com/gentoo/sci/pull/1009 Signed-off-by: Aisha Tammy aisha.cc> sci-biology/khmer/khmer-0.8.ebuild | 39 --- sci-biology/khmer/khmer-1.0.1.ebuild | 62 sci-biology/khmer/khmer-2.1.1.ebuild | 34 sci-biology/khmer/khmer-.ebuild | 42 4 files changed, 34 insertions(+), 143 deletions(-) diff --git a/sci-biology/khmer/khmer-0.8.ebuild b/sci-biology/khmer/khmer-0.8.ebuild deleted file mode 100644 index e19d27e9b..0 --- a/sci-biology/khmer/khmer-0.8.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit distutils-r1 - -DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences" -HOMEPAGE="https://github.com/ged-lab/khmer; -SRC_URI="mirror://pypi/${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..0 --- 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}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -DEPEND="" -RDEPEND="sci-biology/screed" - -python_prepare_all(){ - rm -rf lib/{bzip2,zlib} || die - - sed \ - -e 's:zlib/zlib.h:zlib.h:g' \ - -e 's:bzip2/bzlib.h:bzlib.h:g' \ - -i lib/read_parsers.hh lib/counting.cc || die - - sed \ - -e "/^EXTRA_COMPILE_ARGS/s:=.*:=[]:g" \ - -i setup.py || die - - cat > setup.cfg <<- EOF - [nosetests] - verbosity = 2 - stop = TRUE - attr = !known_failing - - [build_ext] - undef = NO_UNIQUE_RC - libraries = z,bz2 - ## if using system libraries - include-dirs = lib:lib/zlib:lib/bzip2 - # include-dirs = lib - ## if using system libraries (broken) - - define = NDEBUG - # is not needed for most Linux installs - # see the OPT line in /usr/lib/python2.7/config/Makefile which gets included - # in distutils version of CFLAGS - - [easy_install] - - EOF - - distutils-r1_python_prepare_all -} - -python_test() { - esetup.py nosetests || die -} diff --git a/sci-biology/khmer/khmer-2.1.1.ebuild b/sci-biology/khmer/khmer-2.1.1.ebuild new file mode 100644 index 0..11c4231e8 --- /dev/null +++ b/sci-biology/khmer/khmer-2.1.1.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_{7,8,9} ) + +inherit distutils-r1 + +DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences" +HOMEPAGE="https://github.com/dib-lab/khmer; +SRC_URI="mirror://pypi/${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-.ebuild b/sci-biology/khmer/khmer-.ebuild deleted file mode 100644 index
[gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
commit: 30086ecf6e63270161fcb86194fbdae746242fc2 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Sat Jan 20 21:24:14 2018 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sat Jan 20 21:24:14 2018 + 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-.ebuild | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/sci-biology/khmer/khmer-.ebuild b/sci-biology/khmer/khmer-.ebuild index 4cd44c29e..7855665e1 100644 --- a/sci-biology/khmer/khmer-.ebuild +++ b/sci-biology/khmer/khmer-.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"
[gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
commit: adf80768d6a583d418567bb79638a549f997ce08 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Fri Jul 28 19:14:43 2017 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Fri Jul 28 20:05:19 2017 + 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-.ebuild | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/sci-biology/khmer/khmer-.ebuild b/sci-biology/khmer/khmer-.ebuild index cece8e617..4cd44c29e 100644 --- a/sci-biology/khmer/khmer-.ebuild +++ b/sci-biology/khmer/khmer-.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
[gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
commit: 40f710098b525b5dacfd243677dfbe8819655b62 Author: Justin Lecher jlec AT gentoo DOT org AuthorDate: Fri Jun 5 11:05:44 2015 + Commit: Justin Lecher jlec AT gentoo DOT org CommitDate: Fri Jun 5 11:05:44 2015 + 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 j...@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 j...@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=pypikhmer/remote-id +remote-id type=githubged-lab/khmer/remote-id /upstream /pkgmetadata
[gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
commit: 5b0d5724ba788d179d9a596a5e4424f601e5b794 Author: Justin Lecher jlec AT gentoo DOT org AuthorDate: Thu May 15 07:21:06 2014 + Commit: Justin Lecher jlec AT gentoo DOT org CommitDate: Thu May 15 07:21:06 2014 + 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 j...@gentoo.org khmer-0.8.ebuild, + +khmer-1.0.1.ebuild: + Version BUmp + 28 Mar 2014; Martin Mokrejs mmokr...@fold.natur.cuni.cz khmer-.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 +}
[gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
commit: abaea30881541b0d796bf2b6323d49da8ac32e5b Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz AuthorDate: Fri Mar 28 20:13:47 2014 + Commit: Nicolas Bock nicolasbock AT gmail DOT com CommitDate: Mon Mar 31 15:27:34 2014 + 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-.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 mmokr...@fold.natur.cuni.cz khmer-.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 j...@gentoo.org khmer-0.8.ebuild, khmer-.ebuild: Also drop sphinx as build requirement diff --git a/sci-biology/khmer/khmer-.ebuild b/sci-biology/khmer/khmer-.ebuild index 0bd7a8d..f6c6594 100644 --- a/sci-biology/khmer/khmer-.ebuild +++ b/sci-biology/khmer/khmer-.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 +#}
[gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
commit: 2ca96f9db90098568873343a1d1a547bac4eab9a Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz AuthorDate: Fri Mar 28 20:13:47 2014 + Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz CommitDate: Fri Mar 28 20:13:47 2014 + 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-.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 mmokr...@fold.natur.cuni.cz khmer-.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 j...@gentoo.org khmer-0.8.ebuild, khmer-.ebuild: Also drop sphinx as build requirement diff --git a/sci-biology/khmer/khmer-.ebuild b/sci-biology/khmer/khmer-.ebuild index 0bd7a8d..f6c6594 100644 --- a/sci-biology/khmer/khmer-.ebuild +++ b/sci-biology/khmer/khmer-.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 +#}
[gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
commit: a16c385b6548a6575fa667a84071f416a43bbd6b Author: Justin Lecher jlec AT gentoo DOT org AuthorDate: Mon Mar 24 15:23:22 2014 + Commit: Justin Lecher jlec AT gentoo DOT org CommitDate: Mon Mar 24 15:28:29 2014 + 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-.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 j...@gentoo.org khmer-0.8.ebuild, + khmer-.ebuild: + Also drop sphinx as build requirement + 20 Mar 2014; Justin Lecher j...@gentoo.org khmer-0.8.ebuild, khmer-.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-.ebuild b/sci-biology/khmer/khmer-.ebuild index 4bb1d2e..0bd7a8d 100644 --- a/sci-biology/khmer/khmer-.ebuild +++ b/sci-biology/khmer/khmer-.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
[gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
commit: 48368f7f59a39b69831f08f2c9263fbe6e580695 Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz AuthorDate: Sun Mar 16 18:02:30 2014 + Commit: Justin Lecher jlec AT gentoo DOT org CommitDate: Sat Mar 22 09:44:40 2014 + 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-.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 000..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- (16 Mar 2014) + + 16 Mar 2014; Martin Mokrejs mmokr...@fold.natur.cuni.cz +khmer-.ebuild, + +metadata.xml: + sci-biology/khmer: new package diff --git a/sci-biology/khmer/khmer-.ebuild b/sci-biology/khmer/khmer-.ebuild new file mode 100644 index 000..cbd7b2c --- /dev/null +++ b/sci-biology/khmer/khmer-.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 000..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 + herdsci-biology/herd + maintainer +emailmmokr...@fold.natur.cuni.cz/email +nameMartin Mokrejs/name + /maintainer +/pkgmetadata
[gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
commit: bd12b7ef927260f2ce1554ff4a627b68e57938af Author: Justin Lecher jlec AT gentoo DOT org AuthorDate: Tue Mar 18 19:24:38 2014 + Commit: Justin Lecher jlec AT gentoo DOT org CommitDate: Sat Mar 22 09:44:40 2014 + 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-.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 j...@gentoo.org +khmer-0.8.ebuild, + khmer-.ebuild: + Unbundle zlib and bzpi2; bump to disturils-r1; respect CFLAGS + 16 Mar 2014; Martin Mokrejs mmokr...@fold.natur.cuni.cz khmer-.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 000..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}/${P}.tar.gz + +LICENSE=BSD +SLOT=0 +KEYWORDS= ~amd64 ~x86 ~amd64-linux ~x86-linux +IUSE= + +DEPEND= +RDEPEND=sci-biology/screed + +python_prepare_all(){ + rm -rf lib/{bzip2,zlib} || die + + sed \ + -e 's:zlib/zlib.h:zlib.h:g' \ + -e 's:bzip2/bzlib.h:bzlib.h:g' \ + -i lib/read_parsers.hh lib/counting.cc || die + + sed \ + -e /extra_objects/d \ + -e '/libraries/s:, ]:, z, bz2, ]:g' \ + -e s:'-O3',::g \ + -i setup.py || die + + distutils-r1_python_prepare_all +} diff --git a/sci-biology/khmer/khmer-.ebuild b/sci-biology/khmer/khmer-.ebuild index ab29463..4ac1a8b 100644 --- a/sci-biology/khmer/khmer-.ebuild +++ b/sci-biology/khmer/khmer-.ebuild @@ -6,7 +6,7 @@ EAPI=5 PYTHON_COMPAT=( python2_7 ) -inherit distutils git-r3 +inherit distutils-r1 git-r3 DESCRIPTION=In-memory K-mer counting in DNA/RNA/protein sequences HOMEPAGE=https://github.com/ged-lab/khmer; @@ -19,4 +19,21 @@ KEYWORDS= IUSE= DEPEND= -RDEPEND=${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 +}
[gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
commit: 672f6a9b37fc8014c22fe6b8e2d110d52bce7319 Author: Justin Lecher jlec AT gentoo DOT org AuthorDate: Thu Mar 20 09:04:21 2014 + Commit: Justin Lecher jlec AT gentoo DOT org CommitDate: Sat Mar 22 09:44:40 2014 + 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-.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 j...@gentoo.org khmer-0.8.ebuild, + khmer-.ebuild: + Drop nose requirement during build + *khmer-0.8 (18 Mar 2014) 18 Mar 2014; Justin Lecher j...@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-.ebuild b/sci-biology/khmer/khmer-.ebuild index 4ac1a8b..4bb1d2e 100644 --- a/sci-biology/khmer/khmer-.ebuild +++ b/sci-biology/khmer/khmer-.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
[gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
commit: 391aa2b2160b456a7dbbdd34ce72378372615996 Author: Justin Lecher jlec AT gentoo DOT org AuthorDate: Thu Mar 20 09:04:21 2014 + Commit: Justin Lecher jlec AT gentoo DOT org CommitDate: Thu Mar 20 09:04:21 2014 + 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-.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 j...@gentoo.org khmer-0.8.ebuild, + khmer-.ebuild: + Drop nose requirement during build + *khmer-0.8 (18 Mar 2014) 18 Mar 2014; Justin Lecher j...@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-.ebuild b/sci-biology/khmer/khmer-.ebuild index 4ac1a8b..4bb1d2e 100644 --- a/sci-biology/khmer/khmer-.ebuild +++ b/sci-biology/khmer/khmer-.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
[gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
commit: 2fe25927e87d9c3339465453ae165b366ff2d8f2 Author: Justin Lecher jlec AT gentoo DOT org AuthorDate: Tue Mar 18 19:24:38 2014 + Commit: Justin Lecher jlec AT gentoo DOT org CommitDate: Tue Mar 18 19:24:38 2014 + 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-.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 j...@gentoo.org +khmer-0.8.ebuild, + khmer-.ebuild: + Unbundle zlib and bzpi2; bump to disturils-r1; respect CFLAGS + 16 Mar 2014; Martin Mokrejs mmokr...@fold.natur.cuni.cz khmer-.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 000..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}/${P}.tar.gz + +LICENSE=BSD +SLOT=0 +KEYWORDS= ~amd64 ~x86 ~amd64-linux ~x86-linux +IUSE= + +DEPEND= +RDEPEND=sci-biology/screed + +python_prepare_all(){ + rm -rf lib/{bzip2,zlib} || die + + sed \ + -e 's:zlib/zlib.h:zlib.h:g' \ + -e 's:bzip2/bzlib.h:bzlib.h:g' \ + -i lib/read_parsers.hh lib/counting.cc || die + + sed \ + -e /extra_objects/d \ + -e '/libraries/s:, ]:, z, bz2, ]:g' \ + -e s:'-O3',::g \ + -i setup.py || die + + distutils-r1_python_prepare_all +} diff --git a/sci-biology/khmer/khmer-.ebuild b/sci-biology/khmer/khmer-.ebuild index ab29463..4ac1a8b 100644 --- a/sci-biology/khmer/khmer-.ebuild +++ b/sci-biology/khmer/khmer-.ebuild @@ -6,7 +6,7 @@ EAPI=5 PYTHON_COMPAT=( python2_7 ) -inherit distutils git-r3 +inherit distutils-r1 git-r3 DESCRIPTION=In-memory K-mer counting in DNA/RNA/protein sequences HOMEPAGE=https://github.com/ged-lab/khmer; @@ -19,4 +19,21 @@ KEYWORDS= IUSE= DEPEND= -RDEPEND=${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 +}
[gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
commit: 80ae47968e0fdd030a0b9e5816c95d8a741b3a79 Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz AuthorDate: Sun Mar 16 18:02:30 2014 + Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz CommitDate: Sun Mar 16 18:02:30 2014 + 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-.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 000..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- (16 Mar 2014) + + 16 Mar 2014; Martin Mokrejs mmokr...@fold.natur.cuni.cz +khmer-.ebuild, + +metadata.xml: + sci-biology/khmer: new package diff --git a/sci-biology/khmer/khmer-.ebuild b/sci-biology/khmer/khmer-.ebuild new file mode 100644 index 000..cbd7b2c --- /dev/null +++ b/sci-biology/khmer/khmer-.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 000..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 + herdsci-biology/herd + maintainer +emailmmokr...@fold.natur.cuni.cz/email +nameMartin Mokrejs/name + /maintainer +/pkgmetadata
[gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
commit: f4a983de950f873267f37d7ebcd8f01b0a23a05b Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz AuthorDate: Sun Mar 16 18:26:04 2014 + Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz CommitDate: Sun Mar 16 18:26:04 2014 + 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-.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 mmokr...@fold.natur.cuni.cz khmer-.ebuild: + sci-biology/khmer: revert to distutils to obey sandbox violation + *khmer- (16 Mar 2014) 16 Mar 2014; Martin Mokrejs mmokr...@fold.natur.cuni.cz +khmer-.ebuild, diff --git a/sci-biology/khmer/khmer-.ebuild b/sci-biology/khmer/khmer-.ebuild index cbd7b2c..ab29463 100644 --- a/sci-biology/khmer/khmer-.ebuild +++ b/sci-biology/khmer/khmer-.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;