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67 lines
1.5 KiB
67 lines
1.5 KiB
# Copyright 1999-2023 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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DISTUTILS_IN_SOURCE_BUILD=1
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PYTHON_COMPAT=( python3_{9..11} )
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inherit distutils-r1 flag-o-matic
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DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files"
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HOMEPAGE="https://htseq.readthedocs.io/"
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if [[ ${PV} == *9999 ]]; then
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inherit git-r3
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EGIT_REPO_URI="https://github.com/htseq/htseq.git"
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else
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SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.gh.tar.gz"
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S="${WORKDIR}"/htseq-release_${PV}
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KEYWORDS="~amd64"
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fi
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LICENSE="GPL-3+"
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SLOT="0"
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RDEPEND="
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dev-python/numpy[${PYTHON_USEDEP}]
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sci-biology/pysam[${PYTHON_USEDEP}]"
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DEPEND="${RDEPEND}
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test? (
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dev-python/matplotlib[${PYTHON_USEDEP}]
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dev-python/pandas[${PYTHON_USEDEP}]
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dev-python/scipy[${PYTHON_USEDEP}]
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)"
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BDEPEND="
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>=dev-lang/swig-3.0.8
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dev-python/cython[${PYTHON_USEDEP}]"
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distutils_enable_tests pytest
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src_configure() {
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# mask broken asserts in src/step_vector.h:72
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append-cppflags -DNDEBUG
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distutils-r1_src_configure
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}
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python_test() {
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distutils_install_for_testing
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# Due to the build directories creating a competing
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# hierarchy, we move to the test/ dir to avoid implicitly
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# injecting the root HTSeq/ dir into the PYTHONPATH,
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# which leads the python module lookup astray:
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# ${PWD}
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# ├── build
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# │ ├── lib
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# │ │ └── HTSeq
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# │ [...]
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# ├── HTSeq
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# └── test
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cd test/ || die
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ln -s ../example_data || die
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epytest
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}
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