python-biopython: fix build with python 3.13

BioArchLinux/python-biopython/PKGBUILD

@@ -6,7 +6,7 @@
 pkgname=python-biopython
 _pkgname=biopython
 pkgver=1.84
-pkgrel=3
+pkgrel=4
 pkgdesc="Freely available Python tools for computational molecular biology"
 arch=('x86_64')
 url="http://www.biopython.org"
@@ -15,10 +15,18 @@ 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)
-sha512sums=('cadf82959626b2b9f4482757d95d7c4db262d3e1e4a007567a2ed7f1f4114a0d6543886a4971dffbe0ff43579aa7e0c3b7132d8b5e58022e8ddf0b13dbf07f52')
+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 -1 < $srcdir/compat.patch
+}
+
 build() {
   cd "${srcdir}/${_pkgname}-${pkgver}"
   python setup.py build

BioArchLinux/python-biopython/lilac.yaml

@@ -13,3 +13,4 @@ update_on:
   - source: regex
     regex: 'biopython-(\d+.\d+).tar.gz'
     url: "https://github.com/biopython/DIST"
+  - alias: python