py-cutadapt: start upgrade to 5.2

[Thomas Klausner (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Thomas Klausner <wiz%NetBSD.org@localhost>
Pushed By:	wiz
Date:		Wed Nov 12 08:37:56 2025 +0100
Changeset:	54b6e286d2bfd52be1e37ea26c179ce1c12a16f9

Modified Files:
	py-cutadapt/Makefile
	py-cutadapt/PLIST
	py-cutadapt/distinfo

Log Message:
py-cutadapt: start upgrade to 5.2

Fails due to cython problem.
https://github.com/marcelm/cutadapt/issues/864

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=54b6e286d2bfd52be1e37ea26c179ce1c12a16f9

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

diffstat:
 py-cutadapt/Makefile | 15 ++++++---------
 py-cutadapt/PLIST    |  4 ++--
 py-cutadapt/distinfo |  8 ++++----
 3 files changed, 12 insertions(+), 15 deletions(-)

diffs:
diff --git a/py-cutadapt/Makefile b/py-cutadapt/Makefile
index 68b56ff730..d203ec634e 100644
--- a/py-cutadapt/Makefile
+++ b/py-cutadapt/Makefile
@@ -1,6 +1,6 @@
-# $NetBSD$
+# $NetBSD: Makefile,v 1.19 2025/10/09 07:57:24 wiz Exp $
 
-DISTNAME=	cutadapt-4.7
+DISTNAME=	cutadapt-5.2
 PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
 CATEGORIES=	biology python
 MASTER_SITES=	${MASTER_SITE_PYPI:=c/cutadapt/}
@@ -10,19 +10,16 @@ HOMEPAGE=	https://cutadapt.readthedocs.io/en/stable/
 COMMENT=	Find and remove adapter sequences, primers, poly-A tails, etc
 LICENSE=	mit
 
-TOOL_DEPENDS+=	${PYPKGPREFIX}-setuptools-[0-9]*:../../devel/py-setuptools
+TOOL_DEPENDS+=	${PYPKGPREFIX}-setuptools>=78:../../devel/py-setuptools
 TOOL_DEPENDS+=	${PYPKGPREFIX}-setuptools_scm-[0-9]*:../../devel/py-setuptools_scm
-TOOL_DEPENDS+=	${PYPKGPREFIX}-wheel-[0-9]*:../../devel/py-wheel
 # needed for python 3.11 as of cutadapt 3.5 release
 TOOL_DEPENDS+=	${PYPKGPREFIX}-cython-[0-9]*:../../devel/py-cython
 DEPENDS+=	${PYPKGPREFIX}-xopen>=1.6.0:../../devel/py-xopen
-DEPENDS+=	${PYPKGPREFIX}-dnaio>=0.10.0:../../wip/py-dnaio
-
-PYTHON_VERSIONS_INCOMPATIBLE=	27 # py-xopen
-
-USE_PKG_RESOURCES=	yes
+DEPENDS+=	${PYPKGPREFIX}-dnaio>=0.10.0:../../biology/py-dnaio
 
 PYTHON_SELF_CONFLICT=	yes
 
+PYTHON_VERSIONS_INCOMPATIBLE=	310
+
 .include "../../lang/python/wheel.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/py-cutadapt/PLIST b/py-cutadapt/PLIST
index deb85e0075..3edaa3bbb5 100644
--- a/py-cutadapt/PLIST
+++ b/py-cutadapt/PLIST
@@ -1,10 +1,10 @@
-@comment $NetBSD$
+@comment $NetBSD: PLIST,v 1.6 2025/04/15 13:03:38 adam Exp $
 bin/cutadapt
-${PYSITELIB}/${WHEEL_INFODIR}/LICENSE
 ${PYSITELIB}/${WHEEL_INFODIR}/METADATA
 ${PYSITELIB}/${WHEEL_INFODIR}/RECORD
 ${PYSITELIB}/${WHEEL_INFODIR}/WHEEL
 ${PYSITELIB}/${WHEEL_INFODIR}/entry_points.txt
+${PYSITELIB}/${WHEEL_INFODIR}/licenses/LICENSE
 ${PYSITELIB}/${WHEEL_INFODIR}/top_level.txt
 ${PYSITELIB}/cutadapt/__init__.py
 ${PYSITELIB}/cutadapt/__init__.pyc
diff --git a/py-cutadapt/distinfo b/py-cutadapt/distinfo
index 2c8958b396..607581c5bf 100644
--- a/py-cutadapt/distinfo
+++ b/py-cutadapt/distinfo
@@ -1,5 +1,5 @@
-$NetBSD$
+$NetBSD: distinfo,v 1.8 2024/03/16 13:46:42 bacon Exp $
 
-BLAKE2s (cutadapt-4.7.tar.gz) = f5b03c53fc169c1c9398c40ffc34de0b54a79a082df3064035c0780aef5cde8f
-SHA512 (cutadapt-4.7.tar.gz) = 975a12899fc014b645839ab4ebc1cbb9df7c87d4c4bef67976a72b657d7c274a49edf08e7dfa935d893cf7af35027a0cc04ceb79be0766cbe9ca49c5a2a85c61
-Size (cutadapt-4.7.tar.gz) = 250893 bytes
+BLAKE2s (cutadapt-5.2.tar.gz) = 541d28c2c5f5c893af0b4fd8f86c7eb9493ac6f0f9005e1fb9a2e147b7438bdb
+SHA512 (cutadapt-5.2.tar.gz) = 9205e41d7f729eab31c5630788012b0c0d0eb726f3ae45552f0a39f90ac6a9dc1a07c5dc16db38aab873f626186583b3c969154a81574a18683c07494279c48c
+Size (cutadapt-5.2.tar.gz) = 253642 bytes