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python-pybedtools: fix build with python 3.11

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bipin kumar 2023-05-07 11:36:07 +05:30
parent b05a7acaa1
commit 8627020087
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GPG key ID: C67233497C15E476
1 changed files with 19 additions and 7 deletions
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26
BioArchLinux/python-pybedtools/PKGBUILD
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@ -3,13 +3,15 @@
pkgname=python-pybedtools
_base=${pkgname#python-}
pkgver=0.9.0
pkgrel=2
pkgrel=3
pkgdesc="python wrapper for BEDTools bioinformatics suite"
arch=('x86_64')
url="https://github.com/daler/pybedtools"
license=(GPL2)
depends=('bedtools' 'python-numpy' 'python-pandas' 'python-pysam' 'python-six')
makedepends=('cython' 'python-setuptools' 'python-pytest' 'python-pyaml' 'python-yaml' 'python-numpydoc' 'python-sphinx')
depends=('python' 'bedtools' 'python-numpy' 'python-pandas' 'python-pysam' 'python-six' 'glibc' 'gcc-libs' 'zlib' 'python-yaml')
makedepends=('cython' 'python-setuptools' 'python-pytest' 'python-pyaml' 'python-yaml' 'python-numpydoc' 'python-sphinx' 'python-build'
'python-installer'
'python-wheel')
optdepends=(
'htslib: for working with SAM/BAM/CRAM files'
'python-matplotlib: for plotting genomic intervals'
@ -19,14 +21,24 @@ conflicts=('python-pyvcf')
source=(https://pypi.org/packages/source/${_base::1}/${_base}/${_base}-${pkgver}.tar.gz)
sha512sums=('017a2fd3d6d11c26437af0898c5bfa354210d24747e510e5cbbc0584a355cd4b12c123e7b39dc6f6e386608ec0142b37026928d239b085277b79eba91c9a3361')
prepare() {
cd "${_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}-${pkgver}"
python setup.py build
python -m build --wheel --no-isolation
#python setup.py build_ext -i -f
#python setup.py build
}
package() {
cd "${_base}-${pkgver}"
export PYTHONHASHSEED=0
PYTHONPYCACHEPREFIX="${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
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
}