commit: 1cea5dc52d7f3cb7f2451d8e58bef8908b8df687 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Thu Apr 6 19:29:06 2023 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Thu Apr 6 19:29:06 2023 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1cea5dc5
sci-biology/pysam: drop 0.20.0 Closes: https://bugs.gentoo.org/836857 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/pysam/Manifest | 1 - sci-biology/pysam/pysam-0.20.0.ebuild | 69 ----------------------------------- 2 files changed, 70 deletions(-) diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index 0e0b82641fc1..2bc79f89f441 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1,2 +1 @@ -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-0.20.0.ebuild b/sci-biology/pysam/pysam-0.20.0.ebuild deleted file mode 100644 index 6372f1602f70..000000000000 --- a/sci-biology/pysam/pysam-0.20.0.ebuild +++ /dev/null @@ -1,69 +0,0 @@ -# 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 -> ${P}.gh.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="=sci-libs/htslib-1.16*:=" -DEPEND="${RDEPEND} - dev-python/cython[${PYTHON_USEDEP}] - dev-python/setuptools[${PYTHON_USEDEP}]" -BDEPEND=" - test? ( - =sci-biology/bcftools-1.16* - =sci-biology/samtools-1.16* - )" - -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' - # broken test - # https://github.com/pysam-developers/pysam/issues/1151#issuecomment-1365662253 - 'tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope' -) - -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 -}
