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| author |   David Seifert <soap@gentoo.org> | 2022-06-19 10:08:42 +0200 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2022-06-19 10:08:42 +0200 |
| commit | d3866d06942c293186a4fca7108a74c6a54ec10b (patch) | |
| tree | c12e719941dd8ed465b0ac064bd2512a0348f382 /sci-biology | |
| parent | sys-devel/autoconf: update EAPI 6 -> 7 (diff) | |
| download | gentoo-d3866d06942c293186a4fca7108a74c6a54ec10b.tar.gz gentoo-d3866d06942c293186a4fca7108a74c6a54ec10b.tar.bz2 gentoo-d3866d06942c293186a4fca7108a74c6a54ec10b.zip | |
sci-biology/pysam: drop 0.17.0
Signed-off-by: David Seifert <soap@gentoo.org>
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/pysam/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/pysam/pysam-0.17.0.ebuild | 66 |
2 files changed, 0 insertions, 67 deletions
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index 1e0c911e03c6..f1a1fe7298b7 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1,2 +1 @@ -DIST pysam-0.17.0.tar.gz 3579324 BLAKE2B 6b88fe771350f20fa7c90a4c02c60fefd6a34d979c687fce1e34a17e1ff203c7d2d07e36b64f7a73f99676b805334df7f049932ce15e26362a5214da03435d64 SHA512 16740f08fb68a1f24656454b834dd9ac52ad9f864f307564566fc244bbd2efb7cb17107b2e85ca5c56af817918a138d1c071533de1b80e5bba42b01bbad7f552 DIST pysam-0.19.1.gh.tar.gz 3649711 BLAKE2B dac3ab5a86ef95048e966fc007a0aa1c96ca8498f7c2672c2ed024f34b508bac42048e58b8ae0b538cea137a51e1874bb5c2c4976c7f3dc657a4c2cf5f9a27fb SHA512 719f3a15e7dd277a90cce7f938b674ff86ef6b8f2d3440c3a0bf2ea22c4fbc2b3c9e0cf297d958c99e09dcd6e9905f32e8c632158aa8d5af8210e79705e1c479 diff --git a/sci-biology/pysam/pysam-0.17.0.ebuild b/sci-biology/pysam/pysam-0.17.0.ebuild deleted file mode 100644 index afdc4777e20e..000000000000 --- a/sci-biology/pysam/pysam-0.17.0.ebuild +++ /dev/null @@ -1,66 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) - -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 -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="=sci-libs/htslib-1.13*:=" -DEPEND="${RDEPEND} - dev-python/cython[${PYTHON_USEDEP}] - dev-python/setuptools[${PYTHON_USEDEP}]" -BDEPEND=" - test? ( - =sci-biology/bcftools-1.13* - =sci-biology/samtools-1.13* - )" - -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="${EPREFIX}"/usr/include - export HTSLIB_LIBRARY_DIR="${EPREFIX}"/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 -} |