commit: a46d8d048179a0c699775baa9eb4157949e4671c Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Thu Apr 6 18:10:36 2023 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Thu Apr 6 18:10:36 2023 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a46d8d04
sci-biology/pysam: add 0.21.0 Bug: https://bugs.gentoo.org/836857 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/pysam/Manifest | 1 + sci-biology/pysam/pysam-0.21.0.ebuild | 66 +++++++++++++++++++++++++++++++++++ 2 files changed, 67 insertions(+) diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index fc19ef776276..0e0b82641fc1 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1 +1,2 @@ DIST pysam-0.20.0.gh.tar.gz 3748498 BLAKE2B 1c1b99e5ec34641c196dd574e634cc87d49baa594243eca20ad1f99d2c01b8aadead70a729f389c93cf6f5e95f20d9c7e3d050a47821d1b0dcaaff39d88e6825 SHA512 3f8402057e1d5c807886d1d38180dbdbfa8557700fa97bd59cb42df4d7cc461dcbe54808a169ba5f9696651e801fd0431480cd033b601cd4e9c11bf8bbf14e49 +DIST pysam-0.21.0.gh.tar.gz 3842829 BLAKE2B 83db290ec0bae71106276ed4f1721292c0d2fa55053c7451f0a8a79619b1c4d8444b99293ac5d8051bfb0b59e984e32a89798bab091e3a019b7c2a3fb7414d1c SHA512 b2ac986b6a352df1d2066a224d710648a88d8ad44273623a89ae0f4bb2645b00f0d0e1685c8ccedfd379259255957e653f3c3199621ac1d4c26098f538b6bfa7 diff --git a/sci-biology/pysam/pysam-0.21.0.ebuild b/sci-biology/pysam/pysam-0.21.0.ebuild new file mode 100644 index 000000000000..588cd1bc4f1b --- /dev/null +++ b/sci-biology/pysam/pysam-0.21.0.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{9..11} ) + +inherit distutils-r1 + +DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format" +HOMEPAGE=" + https://github.com/pysam-developers/pysam + https://pypi.org/project/pysam/"; +SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="=sci-libs/htslib-1.17*:=" +DEPEND="${RDEPEND} + dev-python/cython[${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}]" +BDEPEND=" + test? ( + =sci-biology/bcftools-1.17* + =sci-biology/samtools-1.17* + )" + +distutils_enable_tests pytest + +DISTUTILS_IN_SOURCE_BUILD=1 + +EPYTEST_DESELECT=( + # only work with bundled htslib + 'tests/tabix_test.py::TestRemoteFileHTTP' + 'tests/tabix_test.py::TestRemoteFileHTTPWithHeader' +) + +python_prepare_all() { + # unbundle htslib + export HTSLIB_MODE="external" + export HTSLIB_INCLUDE_DIR="${ESYSROOT}"/usr/include + export HTSLIB_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir) + rm -r htslib || die + + # prevent setup.py from adding RPATHs (except $ORIGIN) + sed -e '/runtime_library_dirs=htslib_library_dirs/d' \ + -i setup.py || die + + if use test; then + einfo "Building test data" + emake -C tests/pysam_data + emake -C tests/cbcf_data + fi + + distutils-r1_python_prepare_all +} + +python_compile() { + # breaks with parallel build + # need to avoid dropping .so plugins into + # build-lib, which breaks tests + esetup.py build_ext --inplace -j1 + distutils-r1_python_compile -j1 +}
