[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/
commit: 7a7acdb52f5a587412f7f4f51529d6986e47fb9f Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue May 2 12:23:53 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue May 2 12:23:53 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7a7acdb5 sci-biology/pybedtools: disable py3.9 Signed-off-by: Andrew Ammerlaan gentoo.org> sci-biology/pybedtools/pybedtools-0.8.2.ebuild | 2 +- sci-biology/pybedtools/pybedtools-0.9.0.ebuild | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild index 422d74a31..bc02bda6f 100644 --- a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild +++ b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{9..11} ) +PYTHON_COMPAT=( python3_{10..11} ) DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 diff --git a/sci-biology/pybedtools/pybedtools-0.9.0.ebuild b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild index 422d74a31..bc02bda6f 100644 --- a/sci-biology/pybedtools/pybedtools-0.9.0.ebuild +++ b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{9..11} ) +PYTHON_COMPAT=( python3_{10..11} ) DISTUTILS_USE_PEP517=setuptools inherit distutils-r1
[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/
commit: 987fad3d4b257f83e58e20183e324b21e82f1584 Author: Horea Christian chymera eu> AuthorDate: Sat Mar 25 04:23:37 2023 + Commit: Horea Christian gmail com> CommitDate: Sat Mar 25 04:23:37 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=987fad3d sci-biology/pybedtools: add 0.9.0 Signed-off-by: Horea Christian chymera.eu> sci-biology/pybedtools/pybedtools-0.9.0.ebuild | 43 ++ 1 file changed, 43 insertions(+) diff --git a/sci-biology/pybedtools/pybedtools-0.9.0.ebuild b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild new file mode 100644 index 0..422d74a31 --- /dev/null +++ b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{9..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="Use BED and GFF files from python using BEDtools" +HOMEPAGE="https://daler.github.io/pybedtools; +SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + sci-biology/bedtools + sci-biology/pysam[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] +" + +BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" + +# TODO: fix docs building +# ModuleNotFoundError: No module named 'pybedtools.cbedtools' +# even if pybedtools is installed +#distutils_enable_sphinx docs/source +distutils_enable_tests pytest + +python_test() { + # Requires network + local EPYTEST_DESELECT=( + test/test_helpers.py::test_chromsizes + ) + cd "${T}" || die + epytest --pyargs pybedtools +}
[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/
commit: 811db2634692304728d8e765f4a7b5ad5b54f89a Author: Horea Christian chymera eu> AuthorDate: Sat Mar 25 04:19:10 2023 + Commit: Horea Christian gmail com> CommitDate: Sat Mar 25 04:19:10 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=811db263 sci-biology/pybedtools: distutils PEP 517 Signed-off-by: Horea Christian chymera.eu> sci-biology/pybedtools/pybedtools-0.8.2.ebuild | 1 + 1 file changed, 1 insertion(+) diff --git a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild index aca7eb9ed..422d74a31 100644 --- a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild +++ b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild @@ -4,6 +4,7 @@ EAPI=8 PYTHON_COMPAT=( python3_{9..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1
[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/
commit: 50d38d2e487a86cdb5348a6ac81f227ab4b4af12 Author: Horea Christian chymera eu> AuthorDate: Sat Mar 25 04:16:54 2023 + Commit: Horea Christian gmail com> CommitDate: Sat Mar 25 04:17:13 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=50d38d2e sci-biology/pybedtools: enable py3.11, py3.9, fixed tests Signed-off-by: Horea Christian chymera.eu> sci-biology/pybedtools/pybedtools-0.8.2.ebuild | 16 +++- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild index 8f4ae591f..aca7eb9ed 100644 --- a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild +++ b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_10 ) +PYTHON_COMPAT=( python3_{9..11} ) inherit distutils-r1 @@ -15,9 +15,6 @@ LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" -# ModuleNotFoundError: No module named 'pybedtools.cbedtools' -RESTRICT="test" - RDEPEND=" sci-biology/bedtools sci-biology/pysam[${PYTHON_USEDEP}] @@ -34,3 +31,12 @@ BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" # even if pybedtools is installed #distutils_enable_sphinx docs/source distutils_enable_tests pytest + +python_test() { + # Requires network + local EPYTEST_DESELECT=( + test/test_helpers.py::test_chromsizes + ) + cd "${T}" || die + epytest --pyargs pybedtools +}
[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/
commit: b8f4b9f92217f53077630ec58e4fe794669768a3 Author: Andrew Ammerlaan gentoo org> AuthorDate: Sat Jan 15 11:22:53 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Sat Jan 15 11:22:53 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b8f4b9f9 sci-biology/pybedtools: bump to version 0.8.2 Closes: https://github.com/gentoo/sci/issues/983 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan gentoo.org> ...dtools-0.8.0.ebuild => pybedtools-0.8.2.ebuild} | 35 -- 1 file changed, 13 insertions(+), 22 deletions(-) diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild similarity index 54% rename from sci-biology/pybedtools/pybedtools-0.8.0.ebuild rename to sci-biology/pybedtools/pybedtools-0.8.2.ebuild index 6d391b0a8..95bee9be2 100644 --- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild +++ b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{8..10} ) inherit distutils-r1 @@ -14,32 +14,23 @@ SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.g LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="minimal" + +# ModuleNotFoundError: No module named 'pybedtools.cbedtools' RESTRICT="test" -# Tests reported to fail on Gentoo: -# https://github.com/daler/pybedtools/issues/329 -# see requirements.txt RDEPEND=" sci-biology/bedtools - sci-biology/pysam + sci-biology/pysam[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] dev-python/pandas[${PYTHON_USEDEP}] - !minimal? ( sci-libs/htslib )" -# optional-requirements.txt also lists: -# ucsc-bigwigtobedgraph -# ucsc-bedgraphtobigwig -# ucsc-wigtobigwig -BDEPEND="${RDEPEND} - dev-python/cython[${PYTHON_USEDEP}]" - -# ToDo: fix docs building + dev-python/matplotlib[${PYTHON_USEDEP}] +" + +BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" + +# TODO: fix docs building # ModuleNotFoundError: No module named 'pybedtools.cbedtools' # even if pybedtools is installed #distutils_enable_sphinx docs/source distutils_enable_tests pytest - -src_compile(){ - python setup.py cythonize - distutils-r1_src_compile -}
[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/
commit: 45f4ecf6f9d5e9c4e699ea84a7b4b8bb6c9740d6 Author: Andrew Ammerlaan riseup net> AuthorDate: Thu Dec 31 10:34:09 2020 + Commit: Aisha Tammy aisha cc> CommitDate: Thu Dec 31 12:04:10 2020 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=45f4ecf6 sci-biology/pybedtools: drop py3.6 Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> Closes: https://github.com/gentoo/sci/pull/1012 Signed-off-by: Aisha Tammy aisha.cc> sci-biology/pybedtools/pybedtools-0.8.0.ebuild | 32 +++--- 1 file changed, 13 insertions(+), 19 deletions(-) diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild index a91de8cca..6d391b0a8 100644 --- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild +++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild @@ -3,7 +3,7 @@ EAPI=7 -PYTHON_COMPAT=( python3_{6..9} ) +PYTHON_COMPAT=( python3_{7..9} ) inherit distutils-r1 @@ -13,8 +13,8 @@ SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.g LICENSE="MIT" SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="doc minimal" +KEYWORDS="~amd64 ~x86" +IUSE="minimal" RESTRICT="test" # Tests reported to fail on Gentoo: # https://github.com/daler/pybedtools/issues/329 @@ -23,29 +23,23 @@ RESTRICT="test" RDEPEND=" sci-biology/bedtools sci-biology/pysam - dev-python/numpy - dev-python/pandas - !minimal? ( sci-libs/htslib ) - doc? ( dev-python/sphinx )" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + !minimal? ( sci-libs/htslib )" # optional-requirements.txt also lists: # ucsc-bigwigtobedgraph # ucsc-bedgraphtobigwig # ucsc-wigtobigwig -DEPEND="${RDEPEND} +BDEPEND="${RDEPEND} dev-python/cython[${PYTHON_USEDEP}]" +# ToDo: fix docs building +# ModuleNotFoundError: No module named 'pybedtools.cbedtools' +# even if pybedtools is installed +#distutils_enable_sphinx docs/source +distutils_enable_tests pytest + src_compile(){ python setup.py cythonize distutils-r1_src_compile - use doc && cd docs && emake html -} - -src_install(){ - distutils-r1_src_install - if use doc; then - insinto /usr/share/doc/"${PN}" - doins -r docs/build/html - fi } - -distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/
commit: f1b4f4489e2e9181bca1dde19fffb24a9155bef7 Author: Martin Mokrejs gmail com> AuthorDate: Sat Dec 12 15:23:20 2020 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sat Dec 12 15:23:38 2020 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f1b4f448 sci-biology/pybedtools: document more dependencies Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Martin Mokrejs gmail.com> sci-biology/pybedtools/pybedtools-0.8.0.ebuild | 7 +++ 1 file changed, 7 insertions(+) diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild index 9edb8f366..a91de8cca 100644 --- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild +++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild @@ -19,11 +19,18 @@ RESTRICT="test" # Tests reported to fail on Gentoo: # https://github.com/daler/pybedtools/issues/329 +# see requirements.txt RDEPEND=" sci-biology/bedtools sci-biology/pysam + dev-python/numpy + dev-python/pandas !minimal? ( sci-libs/htslib ) doc? ( dev-python/sphinx )" +# optional-requirements.txt also lists: +# ucsc-bigwigtobedgraph +# ucsc-bedgraphtobigwig +# ucsc-wigtobigwig DEPEND="${RDEPEND} dev-python/cython[${PYTHON_USEDEP}]"
[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/
commit: 08cb203ae14acd64b0d0c5a7489d9fca813154de Author: Horea Christian chymera eu> AuthorDate: Sun Sep 27 06:50:26 2020 + Commit: Horea Christian gmail com> CommitDate: Sun Sep 27 06:50:26 2020 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=08cb203a sci-biology/pybedtools: PYTHON_COMPAT update and actually install files Package-Manager: Portage-3.0.8, Repoman-3.0.1 Signed-off-by: Horea Christian chymera.eu> sci-biology/pybedtools/pybedtools-0.8.0.ebuild | 17 - 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild index 440e644b7..9edb8f366 100644 --- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild +++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild @@ -3,7 +3,7 @@ EAPI=7 -PYTHON_COMPAT=( python2_7 python3_{5,6,7,8} ) +PYTHON_COMPAT=( python3_{6..9} ) inherit distutils-r1 @@ -15,6 +15,9 @@ LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="doc minimal" +RESTRICT="test" +# Tests reported to fail on Gentoo: +# https://github.com/daler/pybedtools/issues/329 RDEPEND=" sci-biology/bedtools @@ -26,12 +29,16 @@ DEPEND="${RDEPEND} src_compile(){ python setup.py cythonize - default + distutils-r1_src_compile use doc && cd docs && emake html } src_install(){ - default - insinto /usr/share/doc/"${PN}" - doins -r docs/build/html + distutils-r1_src_install + if use doc; then + insinto /usr/share/doc/"${PN}" + doins -r docs/build/html + fi } + +distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/
commit: 3a0d3cb989aa14f980ad867cb8b7d7db5284789f Author: Martin Mokrejs gmail com> AuthorDate: Wed May 6 18:27:40 2020 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed May 6 18:28:05 2020 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3a0d3cb9 sci-biology/pybedtools: hopefully install generated HTML files Package-Manager: Portage-2.3.95, Repoman-2.3.22 Signed-off-by: Martin Mokrejs gmail.com> sci-biology/pybedtools/pybedtools-0.8.0.ebuild | 6 ++ 1 file changed, 6 insertions(+) diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild index 9d4dc23c0..440e644b7 100644 --- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild +++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild @@ -29,3 +29,9 @@ src_compile(){ default use doc && cd docs && emake html } + +src_install(){ + default + insinto /usr/share/doc/"${PN}" + doins -r docs/build/html +}
[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/
commit: e29df37c8b9b02f3749a57c2075bed05f0a71260 Author: Martin Mokrejs gmail com> AuthorDate: Wed May 6 18:22:00 2020 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed May 6 18:22:20 2020 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e29df37c sci-biology/pybedtools: respect minimal and doc USE flags Installation of the to be generated doc pages is not tested as I am blocked by bug #721306. Probably some dir needs to be recursively installed. Package-Manager: Portage-2.3.95, Repoman-2.3.22 Signed-off-by: Martin Mokrejs gmail.com> sci-biology/pybedtools/pybedtools-0.8.0.ebuild | 7 +-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild index cd444a09e..9d4dc23c0 100644 --- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild +++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild @@ -14,15 +14,18 @@ SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.g LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" +IUSE="doc minimal" RDEPEND=" sci-biology/bedtools - sci-biology/pysam" + sci-biology/pysam + !minimal? ( sci-libs/htslib ) + doc? ( dev-python/sphinx )" DEPEND="${RDEPEND} dev-python/cython[${PYTHON_USEDEP}]" src_compile(){ python setup.py cythonize default + use doc && cd docs && emake html }
[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/
commit: ae5eb7ca6ede7e8579ade25afb8eb005c62ee35a Author: Martin Mokrejs gmail com> AuthorDate: Wed May 6 17:44:42 2020 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed May 6 17:44:49 2020 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ae5eb7ca sci-biology/pybedtools: update homepage, explicitly run cythonize Package-Manager: Portage-2.3.95, Repoman-2.3.22 Signed-off-by: Martin Mokrejs gmail.com> sci-biology/pybedtools/pybedtools-0.8.0.ebuild | 13 ++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild index d817a594f..cd444a09e 100644 --- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild +++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 python3_{5,6,7,8} ) inherit distutils-r1 DESCRIPTION="Use BED and GFF files from python using BEDtools" -HOMEPAGE="http://pythonhosted.org/pybedtools/; +HOMEPAGE="https://daler.github.io/pybedtools; SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.gz" LICENSE="MIT" @@ -16,6 +16,13 @@ SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="" -RDEPEND="sci-biology/bedtools" +RDEPEND=" + sci-biology/bedtools + sci-biology/pysam" DEPEND="${RDEPEND} dev-python/cython[${PYTHON_USEDEP}]" + +src_compile(){ + python setup.py cythonize + default +}
[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/
commit: f54702e57e98ae5f4bf7f867f40dd3ea29157f19 Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Sun Dec 29 11:39:28 2019 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sun Dec 29 11:39:28 2019 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f54702e5 sci-biology/pybedtools: upgrade from 0.6.9 to 0.8.0 0.6.9 was not fully python3 ready, due to https://stackoverflow.com/questions/40367569/dictionary-not-writable-generic-old-setup-py at least Package-Manager: Portage-2.3.75, Repoman-2.3.17 Signed-off-by: Martin Mokrejs fold.natur.cuni.cz> .../{pybedtools-0.6.9.ebuild => pybedtools-0.8.0.ebuild} | 8 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/sci-biology/pybedtools/pybedtools-0.6.9.ebuild b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild similarity index 70% rename from sci-biology/pybedtools/pybedtools-0.6.9.ebuild rename to sci-biology/pybedtools/pybedtools-0.8.0.ebuild index f0d497802..d817a594f 100644 --- a/sci-biology/pybedtools/pybedtools-0.6.9.ebuild +++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild @@ -1,13 +1,13 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -PYTHON_COMPAT=( python2_7 ) +PYTHON_COMPAT=( python2_7 python3_{5,6,7,8} ) inherit distutils-r1 -DESCRIPTION="Wrapper for Aaron Quinlan's BEDtools, plus other useful methods for working" +DESCRIPTION="Use BED and GFF files from python using BEDtools" HOMEPAGE="http://pythonhosted.org/pybedtools/; SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.gz"
[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/
commit: 302d36d9dd56ccda4ceaa0aa6b514609fe39ff6d Author: Justin Lecher jlec AT gentoo DOT org AuthorDate: Sat Jun 6 10:12:45 2015 + Commit: Justin Lecher jlec AT gentoo DOT org CommitDate: Sat Jun 6 10:12:45 2015 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=302d36d9 sci-biology/pybedtools: Add github to remote-id in metadata.xml Package-Manager: portage-2.2.20 sci-biology/pybedtools/ChangeLog| 3 +++ sci-biology/pybedtools/metadata.xml | 3 +++ 2 files changed, 6 insertions(+) diff --git a/sci-biology/pybedtools/ChangeLog b/sci-biology/pybedtools/ChangeLog index d4cc478..2fb878a 100644 --- a/sci-biology/pybedtools/ChangeLog +++ b/sci-biology/pybedtools/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher j...@gentoo.org metadata.xml: + sci-biology/pybedtools: Add github to remote-id in metadata.xml + 13 Apr 2015; Justin Lecher j...@gentoo.org pybedtools-0.6.9.ebuild: sci-biology/pybedtools: Streamline ebuild diff --git a/sci-biology/pybedtools/metadata.xml b/sci-biology/pybedtools/metadata.xml index b7551a6..3352804 100644 --- a/sci-biology/pybedtools/metadata.xml +++ b/sci-biology/pybedtools/metadata.xml @@ -6,4 +6,7 @@ emailmschu@gmail.com/email nameMichael Schubert/name /maintainer + upstream +remote-id type=githubdaler/pybedtools/remote-id + /upstream /pkgmetadata
[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/
commit: 4d506095aa0fa6c96e45346b80f92c34d776afc7 Author: Justin Lecher jlec AT gentoo DOT org AuthorDate: Mon Apr 13 06:20:33 2015 + Commit: Justin Lecher jlec AT gentoo DOT org CommitDate: Mon Apr 13 06:20:33 2015 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4d506095 sci-biology/pybedtools: Streamline ebuild Package-Manager: portage-2.2.18 sci-biology/pybedtools/ChangeLog | 3 +++ sci-biology/pybedtools/pybedtools-0.6.9.ebuild | 7 --- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/sci-biology/pybedtools/ChangeLog b/sci-biology/pybedtools/ChangeLog index 8441cd2..d4cc478 100644 --- a/sci-biology/pybedtools/ChangeLog +++ b/sci-biology/pybedtools/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 13 Apr 2015; Justin Lecher j...@gentoo.org pybedtools-0.6.9.ebuild: + sci-biology/pybedtools: Streamline ebuild + *pybedtools-0.6.9 (12 Apr 2015) 12 Apr 2015; Michael Schubert mschu@gmail.com +metadata.xml, diff --git a/sci-biology/pybedtools/pybedtools-0.6.9.ebuild b/sci-biology/pybedtools/pybedtools-0.6.9.ebuild index 99657ad..1ab30c9 100644 --- a/sci-biology/pybedtools/pybedtools-0.6.9.ebuild +++ b/sci-biology/pybedtools/pybedtools-0.6.9.ebuild @@ -10,12 +10,13 @@ inherit distutils-r1 DESCRIPTION=Wrapper for Aaron Quinlan's BEDtools, plus other useful methods for working HOMEPAGE=http://pythonhosted.org/pybedtools/; -SRC_URI=https://github.com/daler/pybedtools/archive/v${PV}.tar.gz; +SRC_URI=https://github.com/daler/pybedtools/archive/v${PV}.tar.gz - ${P}.tar.gz LICENSE=MIT SLOT=0 +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux IUSE= -DEPEND=sci-biology/bedtools - dev-python/cython[${PYTHON_USEDEP}] RDEPEND=sci-biology/bedtools +DEPEND=${RDEPEND} + dev-python/cython[${PYTHON_USEDEP}]
[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/
commit: 9fad98b6c4ccb13e73afb6d5b6e55854698a252d Author: layman layman AT localhost AuthorDate: Sun Apr 12 16:07:42 2015 + Commit: Justin Lecher jlec AT gentoo DOT org CommitDate: Sun Apr 12 16:07:42 2015 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9fad98b6 sci-biology/pybedtools: add pybedtools Package-Manager: portage-2.2.14-prefix sci-biology/pybedtools/ChangeLog | 9 + sci-biology/pybedtools/metadata.xml| 9 + sci-biology/pybedtools/pybedtools-0.6.9.ebuild | 21 + 3 files changed, 39 insertions(+) diff --git a/sci-biology/pybedtools/ChangeLog b/sci-biology/pybedtools/ChangeLog new file mode 100644 index 000..8441cd2 --- /dev/null +++ b/sci-biology/pybedtools/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/pybedtools +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*pybedtools-0.6.9 (12 Apr 2015) + + 12 Apr 2015; Michael Schubert mschu@gmail.com +metadata.xml, + +pybedtools-0.6.9.ebuild: + sci-biology/pybedtools: add pybedtools diff --git a/sci-biology/pybedtools/metadata.xml b/sci-biology/pybedtools/metadata.xml new file mode 100644 index 000..b7551a6 --- /dev/null +++ b/sci-biology/pybedtools/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 +emailmschu@gmail.com/email +nameMichael Schubert/name + /maintainer +/pkgmetadata diff --git a/sci-biology/pybedtools/pybedtools-0.6.9.ebuild b/sci-biology/pybedtools/pybedtools-0.6.9.ebuild new file mode 100644 index 000..99657ad --- /dev/null +++ b/sci-biology/pybedtools/pybedtools-0.6.9.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION=Wrapper for Aaron Quinlan's BEDtools, plus other useful methods for working +HOMEPAGE=http://pythonhosted.org/pybedtools/; +SRC_URI=https://github.com/daler/pybedtools/archive/v${PV}.tar.gz; + +LICENSE=MIT +SLOT=0 +IUSE= + +DEPEND=sci-biology/bedtools + dev-python/cython[${PYTHON_USEDEP}] +RDEPEND=sci-biology/bedtools