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# Maintainer: Bipin Kumar <kbipinkumar@pm.me>
# Contributor: Clint Valentine <valentine.clint@gmail.com>
pkgname=python-pybedtools
_base=${pkgname#python-}
pkgver=0.10.0
pkgrel=1
pkgdesc="python wrapper for BEDTools bioinformatics suite"
arch=('x86_64')
url="https://github.com/daler/pybedtools"
license=(GPL2)
depends=('python' 'bedtools' 'python-numpy' 'python-pandas' 'python-pysam' 'python-six' 'glibc' 'gcc-libs' 'zlib' 'python-yaml')
makedepends=('cython' 'python-setuptools' 'python-pytest' 'python-pyaml' 'python-yaml' 'python-numpydoc' 'python-sphinx' 'python-build'
'python-installer'
'python-wheel')
optdepends=(
'htslib: for working with SAM/BAM/CRAM files'
'python-matplotlib: for plotting genomic intervals'
'ucsc-genome-browser: for bedgraph to bigwig conversions')
provides=('python-pyvcf')
conflicts=('python-pyvcf')
source=(https://pypi.org/packages/source/${_base::1}/${_base}/${_base}-${pkgver}.tar.gz)
sha512sums=('f5d164be1499b34417e5e6d29a0300c105b885504a6198d3ba3313f6a0d8777161d0f7dcac887518c5828c013b8dbf5a2b7fd244e49ed39f1c4edbcbf9e2024d')
prepare() {
cd "${_base}-${pkgver}"
# delete the cython-generated extensions to force rebuild against python 3.11
rm pybedtools/cbedtools.cpp
rm pybedtools/featurefuncs.cpp
}
build() {
cd "${_base}-${pkgver}"
python -m build --wheel --no-isolation
#python setup.py build_ext -i -f
#python setup.py build
}
package() {
cd "${_base}-${pkgver}"
python -m installer --destdir="$pkgdir" dist/*.whl
#export PYTHONHASHSEED=0
#PYTHONPYCACHEPREFIX="${PWD}/.cache/cpython/" python setup.py install --prefix=/usr --root="${pkgdir}" --optimize=1 --skip-build
#python setup.py install --prefix=/usr --root="${pkgdir}" --optimize=1 --skip-build
}
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