CVS commit: pkgsrc/biology/py-cutadapt

["Thomas Klausner" <wiz%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   wiz
Date:           Wed Nov 16 23:02:14 UTC 2022

Modified Files:
        pkgsrc/biology/py-cutadapt: Makefile

Log Message:
py-cutadapt: fix build with python 3.11


To generate a diff of this commit:
cvs rdiff -u -r1.9 -r1.10 pkgsrc/biology/py-cutadapt/Makefile

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/py-cutadapt/Makefile
diff -u pkgsrc/biology/py-cutadapt/Makefile:1.9 pkgsrc/biology/py-cutadapt/Makefile:1.10
--- pkgsrc/biology/py-cutadapt/Makefile:1.9     Mon Jan 17 09:03:10 2022
+++ pkgsrc/biology/py-cutadapt/Makefile Wed Nov 16 23:02:14 2022
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.9 2022/01/17 09:03:10 adam Exp $
+# $NetBSD: Makefile,v 1.10 2022/11/16 23:02:14 wiz Exp $
 
 DISTNAME=      cutadapt-3.5
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
@@ -11,6 +11,8 @@ COMMENT=      Find and remove adapter sequenc
 LICENSE=       mit
 
 TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools_scm-[0-9]*:../../devel/py-setuptools_scm
+# needed for python 3.11 as of 3.5 release
+TOOL_DEPENDS+= ${PYPKGPREFIX}-cython-[0-9]*:../../devel/py-cython
 DEPENDS+=      ${PYPKGPREFIX}-dnaio>=0.5.0:../../biology/py-dnaio
 DEPENDS+=      ${PYPKGPREFIX}-xopen>=1.0.0:../../devel/py-xopen
 
@@ -18,6 +20,11 @@ PYTHON_VERSIONS_INCOMPATIBLE=        27 # py-xo
 
 USE_PKG_RESOURCES=     yes
 
+# these files do not support python 3.11 in the 3.5 release
+post-extract:
+       ${RM} ${WRKSRC}/src/cutadapt/*.c
+       cd ${WRKSRC} && cythonize-${PYVERSSUFFIX} src/cutadapt/*.pyx
+
 post-install:
        cd ${DESTDIR}${PREFIX}/bin && \
        ${MV} cutadapt cutadapt-${PYVERSSUFFIX} || ${TRUE}