PKGBUILD


1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46

# Maintainer: Bipin Kumar <kbipinkumar@pm.me>
# Contributor: Evgeniy Alekseev <arcanis.arch at gmail dot com>
# Contributor: Stunts <f.pinamartins at gmail dot com>
# Contributor: damir <damir at archlinux dot org>

pkgname=python-biopython
_pkgname=biopython
pkgver=1.84
pkgrel=5
pkgdesc="Freely available Python tools for computational molecular biology"
arch=('x86_64')
url="http://www.biopython.org"
license=('custom')
makedepends=('python-setuptools')
checkdepends=('python-scipy' 'python-rdflib' 'python-igraph' 'python-reportlab' 'python-networkx' 'python-mmtf' 'python-matplotlib' 'python-coverage')
depends=('python-numpy')
optdepends=('python-mysql-connector: for BioSQL module')
source=("http://www.biopython.org/DIST/${_pkgname}-${pkgver}.tar.gz"
        "compat.patch::https://patch-diff.githubusercontent.com/raw/biopython/biopython/pull/4706.patch")
sha512sums=('cadf82959626b2b9f4482757d95d7c4db262d3e1e4a007567a2ed7f1f4114a0d6543886a4971dffbe0ff43579aa7e0c3b7132d8b5e58022e8ddf0b13dbf07f52'
            '8bd596602458a07857f4bbaf27dab71c6fc563417c68cefb98de2cbb9607eca5748546ae34c94e84a9f2620f31d6a93ffb80e7477c97fc324e01fdbd005f9352')
options=(!debug)

prepare() {
  cd "${srcdir}/${_pkgname}-${pkgver}"
  # python 3.13 compability patch until biopython 1.85 is released
  patch -p1 < $srcdir/compat.patch
}

build() {
  cd "${srcdir}/${_pkgname}-${pkgver}"
  python setup.py build
}

check() {
  local pyver=$(python -c 'import sys; print(*sys.version_info[:2], sep="")')
  local impl=$(python -c 'import platform; print(platform.python_implementation().lower())')
  local machine=$(python -c 'import platform; print(platform.machine())')
  cd "${srcdir}/${_pkgname}-${pkgver}"
  python setup.py test
}
package() {
  cd "${srcdir}/${_pkgname}-${pkgver}"
  python setup.py install --root="${pkgdir}"
  install -Dm644 "LICENSE.rst" "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
}