diff options
| author |   David Seifert <soap@gentoo.org> | 2023-02-19 16:44:18 +0100 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2023-02-19 16:44:18 +0100 |
| commit | 3fa05869a3f147c226aa4dcfcc87c2d7919cf1b5 (patch) | |
| tree | d902e2b63c14522eb6bc513b0bb4343bae08198e /sci-biology/pysam | |
| parent | app-editors/emacs: add 28.3_rc1 (diff) | |
| download | gentoo-3fa05869a3f147c226aa4dcfcc87c2d7919cf1b5.tar.gz gentoo-3fa05869a3f147c226aa4dcfcc87c2d7919cf1b5.tar.bz2 gentoo-3fa05869a3f147c226aa4dcfcc87c2d7919cf1b5.zip | |
sci-biology/pysam: drop 0.19.1
Signed-off-by: David Seifert <soap@gentoo.org>
Diffstat (limited to 'sci-biology/pysam')
| -rw-r--r-- | sci-biology/pysam/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/pysam/pysam-0.19.1.ebuild | 66 |
2 files changed, 0 insertions, 67 deletions
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index fc762c874c2d..fc19ef776276 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1,2 +1 @@ -DIST pysam-0.19.1.gh.tar.gz 3649711 BLAKE2B dac3ab5a86ef95048e966fc007a0aa1c96ca8498f7c2672c2ed024f34b508bac42048e58b8ae0b538cea137a51e1874bb5c2c4976c7f3dc657a4c2cf5f9a27fb SHA512 719f3a15e7dd277a90cce7f938b674ff86ef6b8f2d3440c3a0bf2ea22c4fbc2b3c9e0cf297d958c99e09dcd6e9905f32e8c632158aa8d5af8210e79705e1c479 DIST pysam-0.20.0.gh.tar.gz 3748498 BLAKE2B 1c1b99e5ec34641c196dd574e634cc87d49baa594243eca20ad1f99d2c01b8aadead70a729f389c93cf6f5e95f20d9c7e3d050a47821d1b0dcaaff39d88e6825 SHA512 3f8402057e1d5c807886d1d38180dbdbfa8557700fa97bd59cb42df4d7cc461dcbe54808a169ba5f9696651e801fd0431480cd033b601cd4e9c11bf8bbf14e49 diff --git a/sci-biology/pysam/pysam-0.19.1.ebuild b/sci-biology/pysam/pysam-0.19.1.ebuild deleted file mode 100644 index 1164fd6bc091..000000000000 --- a/sci-biology/pysam/pysam-0.19.1.ebuild +++ /dev/null @@ -1,66 +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 -> ${P}.gh.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="=sci-libs/htslib-1.15.1*:=" -DEPEND="${RDEPEND} - dev-python/cython[${PYTHON_USEDEP}] - dev-python/setuptools[${PYTHON_USEDEP}]" -BDEPEND=" - test? ( - =sci-biology/bcftools-1.15.1* - =sci-biology/samtools-1.15.1* - )" - -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 -} |