commit: 45eacba59a5cb5bfd342b49cd30677887efac7f0 Author: Michael Schubert <mschu.dev <AT> gmail <DOT> com> AuthorDate: Fri Jul 19 08:51:36 2024 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Fri Jul 19 12:35:08 2024 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=45eacba5
dev-python/bedtools: move from sci-biology, version bump 0.10.0 Signed-off-by: Michael Schubert <mschu.dev <AT> gmail.com> Closes: https://github.com/gentoo/sci/pull/1285 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> .../pybedtools/metadata.xml | 0 .../pybedtools/pybedtools-0.10.0.ebuild | 8 ++-- profiles/updates/2Q-2024 | 1 + sci-biology/pybedtools/pybedtools-0.9.0.ebuild | 43 ---------------------- 4 files changed, 4 insertions(+), 48 deletions(-) diff --git a/sci-biology/pybedtools/metadata.xml b/dev-python/pybedtools/metadata.xml similarity index 100% rename from sci-biology/pybedtools/metadata.xml rename to dev-python/pybedtools/metadata.xml diff --git a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild b/dev-python/pybedtools/pybedtools-0.10.0.ebuild similarity index 88% rename from sci-biology/pybedtools/pybedtools-0.8.2.ebuild rename to dev-python/pybedtools/pybedtools-0.10.0.ebuild index bc02bda6f..ae51c24ce 100644 --- a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild +++ b/dev-python/pybedtools/pybedtools-0.10.0.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_{10..12} ) DISTUTILS_USE_PEP517=setuptools - +DISTUTILS_EXT=1 inherit distutils-r1 DESCRIPTION="Use BED and GFF files from python using BEDtools" @@ -25,8 +25,6 @@ RDEPEND=" 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 diff --git a/profiles/updates/2Q-2024 b/profiles/updates/2Q-2024 index bf7fb5174..ad60545f3 100644 --- a/profiles/updates/2Q-2024 +++ b/profiles/updates/2Q-2024 @@ -1 +1,2 @@ move sci-biology/pyfaidx dev-python/pyfaidx +move sci-biology/pybedtools dev-python/pybedtools diff --git a/sci-biology/pybedtools/pybedtools-0.9.0.ebuild b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild deleted file mode 100644 index bc02bda6f..000000000 --- a/sci-biology/pybedtools/pybedtools-0.9.0.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..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 -}
