commit: 45b11a00d7dd6f99521af35a08cc4c7214656751 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat Jul 2 13:16:00 2022 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat Jul 2 13:16:00 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=45b11a00
sci-biology/HTSeq: add 2.0.2 Bug: https://bugs.gentoo.org/809662 Bug: https://bugs.gentoo.org/846221 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/HTSeq/HTSeq-2.0.2.ebuild | 68 ++++++++++++++++++++++++++++++++++++ sci-biology/HTSeq/Manifest | 1 + 2 files changed, 69 insertions(+) diff --git a/sci-biology/HTSeq/HTSeq-2.0.2.ebuild b/sci-biology/HTSeq/HTSeq-2.0.2.ebuild new file mode 100644 index 000000000000..678968788ff7 --- /dev/null +++ b/sci-biology/HTSeq/HTSeq-2.0.2.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_IN_SOURCE_BUILD=1 +PYTHON_COMPAT=( python3_{8..10} ) + +inherit distutils-r1 flag-o-matic + +DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files" +HOMEPAGE="https://htseq.readthedocs.io/"; + +if [[ ${PV} == *9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/htseq/htseq.git"; +else + SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.gh.tar.gz" + + S="${WORKDIR}"/htseq-release_${PV} + KEYWORDS="~amd64" +fi + +LICENSE="GPL-3+" +SLOT="0" +IUSE="test" +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + sci-biology/pysam[${PYTHON_USEDEP}]" +DEPEND="${RDEPEND} + test? ( + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + )" +BDEPEND=" + >=dev-lang/swig-3.0.8 + dev-python/cython[${PYTHON_USEDEP}]" + +distutils_enable_tests pytest + +src_configure() { + # mask broken asserts in src/step_vector.h:72 + append-cppflags -DNDEBUG + + distutils-r1_src_configure +} + +python_test() { + distutils_install_for_testing + + # Due to the build directories creating a competing + # hierarchy, we move to the test/ dir to avoid implicitly + # injecting the root HTSeq/ dir into the PYTHONPATH, + # which leads the python module lookup astray: + # ${PWD} + # ├── build + # │ ├── lib + # │ │ └── HTSeq + # │ [...] + # ├── HTSeq + # └── test + cd test/ || die + ln -s ../example_data || die + epytest +} diff --git a/sci-biology/HTSeq/Manifest b/sci-biology/HTSeq/Manifest index 92258c60174f..fbb304f1410e 100644 --- a/sci-biology/HTSeq/Manifest +++ b/sci-biology/HTSeq/Manifest @@ -1 +1,2 @@ DIST HTSeq-0.12.4.tar.gz 36187218 BLAKE2B 27be4e8783f9e32c10e23ae812069b489eb11dfa4058db43b5db4b8089792351901255103e4d4de1bcf866da3acd13e742adf8d35a9b70305aa156c70dde0837 SHA512 ec4a1a7e9177f103465840ffa9f936a5e887ffd17760b99d4cbdfd5a88e2ab44275fadfcbee153aadc6e828de7be205ed7a07f3a0548457b7c66826341c3ca64 +DIST HTSeq-2.0.2.gh.tar.gz 48468261 BLAKE2B c68ec67906f3cf78954e94214b82fd51bc19e0c505f994a3df4bfc682d804fa26f4883e9a8fa1e8ddf1e4f8ba8690d605705ebdd2d1695470984c2f04b6a19ce SHA512 96c0b4de6c9cfa9e405f02e366ecfed63bb0dba0ab76fe872f6f48b52a4956b08fa75efa4b1e4c6e4560e34b4e2921bf1ec9671831226ad415ed421a88ec3f6d
