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| author | V3n3RiX <venerix@koprulu.sector> | 2024-05-25 00:07:14 +0100 |
|---|---|---|
| committer | V3n3RiX <venerix@koprulu.sector> | 2024-05-25 00:07:14 +0100 |
| commit | f8999218b5a6eafa151e7367030cbfdb69e045ed (patch) | |
| tree | 0d0e9293bcb75153cd18542369fa789ede9338a0 /sci-biology/pysam/pysam-0.21.0.ebuild | |
| parent | aa4954f71a3ba2293395a8cce2321a70c39c7554 (diff) | |
gentoo auto-resync : 25:05:2024 - 00:07:14
Diffstat (limited to 'sci-biology/pysam/pysam-0.21.0.ebuild')
| -rw-r--r-- | sci-biology/pysam/pysam-0.21.0.ebuild | 72 |
1 files changed, 0 insertions, 72 deletions
diff --git a/sci-biology/pysam/pysam-0.21.0.ebuild b/sci-biology/pysam/pysam-0.21.0.ebuild deleted file mode 100644 index 77292ed29613..000000000000 --- a/sci-biology/pysam/pysam-0.21.0.ebuild +++ /dev/null @@ -1,72 +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 -> ${P}.gh.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="=sci-libs/htslib-1.17*:=" -DEPEND="${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 - -PATCHES=( - # backport - # https://github.com/pysam-developers/pysam/commit/17bb13dcfdb56ac238458dcef23fe01893a892e9 - "${FILESDIR}"/${P}-cython-3.patch -) - -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 -} |