commit: b8f4b9f92217f53077630ec58e4fe794669768a3 Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Sat Jan 15 11:22:53 2022 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Sat Jan 15 11:22:53 2022 +0000 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 <andrewammerlaan <AT> 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 -}
