CVS commit: pkgsrc/biology/py-cutadapt

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/biology/py-cutadapt
From: "Jason Bacon" <bacon%netbsd.org@localhost>
Date: Sat, 10 Feb 2024 13:12:35 +0000

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sat Feb 10 13:12:35 UTC 2024

Modified Files:
        pkgsrc/biology/py-cutadapt: DESCR Makefile PLIST distinfo
Removed Files:
        pkgsrc/biology/py-cutadapt: ALTERNATIVES

Log Message:
biology/py-cutadapt: Update to 4.6

Numerous bug fixes and enhancements since 3.5
Changes: https://github.com/marcelm/cutadapt/tags

Also replaced ALTERNATIVES with PYTHON_SELF_CONFLICT
ALTERNATIVES does not work automatically and there is no reason
to have more than one installation of py-cutadapt


To generate a diff of this commit:
cvs rdiff -u -r1.1 -r0 pkgsrc/biology/py-cutadapt/ALTERNATIVES
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/py-cutadapt/DESCR
cvs rdiff -u -r1.10 -r1.11 pkgsrc/biology/py-cutadapt/Makefile
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/py-cutadapt/PLIST
cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/py-cutadapt/distinfo

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/DESCR
diff -u pkgsrc/biology/py-cutadapt/DESCR:1.1 pkgsrc/biology/py-cutadapt/DESCR:1.2
--- pkgsrc/biology/py-cutadapt/DESCR:1.1        Mon Feb  8 01:55:23 2021
+++ pkgsrc/biology/py-cutadapt/DESCR    Sat Feb 10 13:12:35 2024
@@ -1,2 +1,3 @@
-Cutadapt finds and removes adapter sequences, primers, poly-A tails and other
-types of unwanted sequence from your high-throughput sequencing reads.
+Cutadapt finds and removes adapter sequences, primers, poly-A tails
+and other types of unwanted sequence from your high-throughput
+sequencing reads.

Index: pkgsrc/biology/py-cutadapt/Makefile
diff -u pkgsrc/biology/py-cutadapt/Makefile:1.10 pkgsrc/biology/py-cutadapt/Makefile:1.11
--- pkgsrc/biology/py-cutadapt/Makefile:1.10    Wed Nov 16 23:02:14 2022
+++ pkgsrc/biology/py-cutadapt/Makefile Sat Feb 10 13:12:35 2024
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.10 2022/11/16 23:02:14 wiz Exp $
+# $NetBSD: Makefile,v 1.11 2024/02/10 13:12:35 bacon Exp $
 
-DISTNAME=      cutadapt-3.5
+DISTNAME=      cutadapt-4.6
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
 CATEGORIES=    biology python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=c/cutadapt/}
@@ -11,23 +11,16 @@ 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
+# needed for python 3.11 as of cutadapt 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
+DEPENDS+=      ${PYPKGPREFIX}-xopen>=1.6.0:../../devel/py-xopen
+DEPENDS+=      ${PYPKGPREFIX}-dnaio>=0.10.0:../../biology/py-dnaio
 
 PYTHON_VERSIONS_INCOMPATIBLE=  27 # py-xopen
 
 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}
+PYTHON_SELF_CONFLICT=  yes
 
-.include "../../lang/python/egg.mk"
+.include "../../lang/python/wheel.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/biology/py-cutadapt/PLIST
diff -u pkgsrc/biology/py-cutadapt/PLIST:1.3 pkgsrc/biology/py-cutadapt/PLIST:1.4
--- pkgsrc/biology/py-cutadapt/PLIST:1.3        Mon Jan 17 09:03:10 2022
+++ pkgsrc/biology/py-cutadapt/PLIST    Sat Feb 10 13:12:35 2024
@@ -1,18 +1,24 @@
-@comment $NetBSD: PLIST,v 1.3 2022/01/17 09:03:10 adam Exp $
-bin/cutadapt-${PYVERSSUFFIX}
-${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
-${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
-${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
-${PYSITELIB}/${EGG_INFODIR}/entry_points.txt
-${PYSITELIB}/${EGG_INFODIR}/requires.txt
-${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+@comment $NetBSD: PLIST,v 1.4 2024/02/10 13:12:35 bacon 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}/top_level.txt
 ${PYSITELIB}/cutadapt/__init__.py
 ${PYSITELIB}/cutadapt/__init__.pyc
 ${PYSITELIB}/cutadapt/__init__.pyo
 ${PYSITELIB}/cutadapt/__main__.py
 ${PYSITELIB}/cutadapt/__main__.pyc
 ${PYSITELIB}/cutadapt/__main__.pyo
+${PYSITELIB}/cutadapt/_align.pyi
 ${PYSITELIB}/cutadapt/_align.so
+${PYSITELIB}/cutadapt/_kmer_finder.pyi
+${PYSITELIB}/cutadapt/_kmer_finder.so
+${PYSITELIB}/cutadapt/_match_tables.py
+${PYSITELIB}/cutadapt/_match_tables.pyc
+${PYSITELIB}/cutadapt/_match_tables.pyo
 ${PYSITELIB}/cutadapt/_version.py
 ${PYSITELIB}/cutadapt/_version.pyc
 ${PYSITELIB}/cutadapt/_version.pyo
@@ -22,12 +28,20 @@ ${PYSITELIB}/cutadapt/adapters.pyo
 ${PYSITELIB}/cutadapt/align.py
 ${PYSITELIB}/cutadapt/align.pyc
 ${PYSITELIB}/cutadapt/align.pyo
-${PYSITELIB}/cutadapt/filters.py
-${PYSITELIB}/cutadapt/filters.pyc
-${PYSITELIB}/cutadapt/filters.pyo
+${PYSITELIB}/cutadapt/cli.py
+${PYSITELIB}/cutadapt/cli.pyc
+${PYSITELIB}/cutadapt/cli.pyo
+${PYSITELIB}/cutadapt/files.py
+${PYSITELIB}/cutadapt/files.pyc
+${PYSITELIB}/cutadapt/files.pyo
+${PYSITELIB}/cutadapt/info.pyi
+${PYSITELIB}/cutadapt/info.so
 ${PYSITELIB}/cutadapt/json.py
 ${PYSITELIB}/cutadapt/json.pyc
 ${PYSITELIB}/cutadapt/json.pyo
+${PYSITELIB}/cutadapt/kmer_heuristic.py
+${PYSITELIB}/cutadapt/kmer_heuristic.pyc
+${PYSITELIB}/cutadapt/kmer_heuristic.pyo
 ${PYSITELIB}/cutadapt/log.py
 ${PYSITELIB}/cutadapt/log.pyc
 ${PYSITELIB}/cutadapt/log.pyo
@@ -40,10 +54,17 @@ ${PYSITELIB}/cutadapt/parser.pyo
 ${PYSITELIB}/cutadapt/pipeline.py
 ${PYSITELIB}/cutadapt/pipeline.pyc
 ${PYSITELIB}/cutadapt/pipeline.pyo
+${PYSITELIB}/cutadapt/predicates.py
+${PYSITELIB}/cutadapt/predicates.pyc
+${PYSITELIB}/cutadapt/predicates.pyo
+${PYSITELIB}/cutadapt/qualtrim.pyi
 ${PYSITELIB}/cutadapt/qualtrim.so
 ${PYSITELIB}/cutadapt/report.py
 ${PYSITELIB}/cutadapt/report.pyc
 ${PYSITELIB}/cutadapt/report.pyo
+${PYSITELIB}/cutadapt/runners.py
+${PYSITELIB}/cutadapt/runners.pyc
+${PYSITELIB}/cutadapt/runners.pyo
 ${PYSITELIB}/cutadapt/statistics.py
 ${PYSITELIB}/cutadapt/statistics.pyc
 ${PYSITELIB}/cutadapt/statistics.pyo

Index: pkgsrc/biology/py-cutadapt/distinfo
diff -u pkgsrc/biology/py-cutadapt/distinfo:1.6 pkgsrc/biology/py-cutadapt/distinfo:1.7
--- pkgsrc/biology/py-cutadapt/distinfo:1.6     Mon Jan 17 09:03:10 2022
+++ pkgsrc/biology/py-cutadapt/distinfo Sat Feb 10 13:12:35 2024
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.6 2022/01/17 09:03:10 adam Exp $
+$NetBSD: distinfo,v 1.7 2024/02/10 13:12:35 bacon Exp $
 
-BLAKE2s (cutadapt-3.5.tar.gz) = acfca3b84b2ef7d1cf030b288dd4ea464f8c3243c1566a354f5113a92c2799a1
-SHA512 (cutadapt-3.5.tar.gz) = 7ffb2afc1fd57cd30c4c618db0c1c3dde3803bff19709b158537a46c50b4ddc367abf5707e876f139ba5ad1dc18122fa5b69a1db019c03ed7b605cfbb222ef66
-Size (cutadapt-3.5.tar.gz) = 303774 bytes
+BLAKE2s (cutadapt-4.6.tar.gz) = 5a77d2a4b39e59f207c330cfd74641a228940dea50e36f6673b341ec432f57ec
+SHA512 (cutadapt-4.6.tar.gz) = b7ab31c6df72d970625edbf3dd0d0970a99c1a044b898449ec059d261db6f64b1b756a8a937217fb3f298cf4cb002c4a8c616402ec7dbc28fc2cc16ea05c2faf
+Size (cutadapt-4.6.tar.gz) = 250254 bytes

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