From adb1e3db7fef9c36231478417baf3c49f4c256bf Mon Sep 17 00:00:00 2001
From: Jason Bacon <bacon@NetBSD.org>
Date: Tue, 8 Oct 2019 19:20:43 -0500
Subject: [PATCH] py-cutadapt: Upgrade to 2.5

---
 py-cutadapt/Makefile |  4 +--
 py-cutadapt/PLIST    | 64 +++++++++++++++++++++-----------------------
 py-cutadapt/distinfo |  8 +++---
 3 files changed, 35 insertions(+), 41 deletions(-)

diff --git a/py-cutadapt/Makefile b/py-cutadapt/Makefile
index f089b76519..14792fbed4 100644
--- a/py-cutadapt/Makefile
+++ b/py-cutadapt/Makefile
@@ -4,7 +4,7 @@
 #               Generated by fbsd2pkg                     #
 ###########################################################
 
-DISTNAME=	cutadapt-${PORTVERSION}
+DISTNAME=	cutadapt-2.5
 PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_PYPI:=c/cutadapt/}
@@ -19,7 +19,5 @@ DEPENDS+=	${PYPKGPREFIX}-xopen>=0:../../devel/py-xopen
 USE_LANGUAGES=	c
 PYDISTUTILSPKG=	yes
 
-PORTVERSION=	1.14
-
 .include "../../lang/python/egg.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/py-cutadapt/PLIST b/py-cutadapt/PLIST
index b8a188efe4..f1052a859b 100644
--- a/py-cutadapt/PLIST
+++ b/py-cutadapt/PLIST
@@ -7,44 +7,40 @@ ${PYSITELIB}/${EGG_INFODIR}/entry_points.txt
 ${PYSITELIB}/${EGG_INFODIR}/requires.txt
 ${PYSITELIB}/${EGG_INFODIR}/top_level.txt
 ${PYSITELIB}/cutadapt/__init__.py
-${PYSITELIB}/cutadapt/__init__.pyc
+${PYSITELIB}/cutadapt/__main__.py
 ${PYSITELIB}/cutadapt/__init__.pyo
-${PYSITELIB}/cutadapt/_align.so
-${PYSITELIB}/cutadapt/_qualtrim.so
-${PYSITELIB}/cutadapt/_seqio.so
-${PYSITELIB}/cutadapt/_version.py
-${PYSITELIB}/cutadapt/_version.pyc
+${PYSITELIB}/cutadapt/__init__.pyc
+${PYSITELIB}/cutadapt/__main__.pyo
+${PYSITELIB}/cutadapt/__main__.pyc
 ${PYSITELIB}/cutadapt/_version.pyo
-${PYSITELIB}/cutadapt/adapters.py
-${PYSITELIB}/cutadapt/adapters.pyc
+${PYSITELIB}/cutadapt/_version.pyc
 ${PYSITELIB}/cutadapt/adapters.pyo
-${PYSITELIB}/cutadapt/align.py
-${PYSITELIB}/cutadapt/align.pyc
+${PYSITELIB}/cutadapt/adapters.pyc
 ${PYSITELIB}/cutadapt/align.pyo
-${PYSITELIB}/cutadapt/colorspace.py
-${PYSITELIB}/cutadapt/colorspace.pyc
-${PYSITELIB}/cutadapt/colorspace.pyo
-${PYSITELIB}/cutadapt/compat.py
-${PYSITELIB}/cutadapt/compat.pyc
-${PYSITELIB}/cutadapt/compat.pyo
-${PYSITELIB}/cutadapt/filters.py
-${PYSITELIB}/cutadapt/filters.pyc
+${PYSITELIB}/cutadapt/align.pyc
 ${PYSITELIB}/cutadapt/filters.pyo
-${PYSITELIB}/cutadapt/modifiers.py
-${PYSITELIB}/cutadapt/modifiers.pyc
+${PYSITELIB}/cutadapt/filters.pyc
+${PYSITELIB}/cutadapt/log.pyo
+${PYSITELIB}/cutadapt/log.pyc
 ${PYSITELIB}/cutadapt/modifiers.pyo
-${PYSITELIB}/cutadapt/qualtrim.py
-${PYSITELIB}/cutadapt/qualtrim.pyc
-${PYSITELIB}/cutadapt/qualtrim.pyo
-${PYSITELIB}/cutadapt/report.py
-${PYSITELIB}/cutadapt/report.pyc
+${PYSITELIB}/cutadapt/modifiers.pyc
+${PYSITELIB}/cutadapt/parser.pyo
+${PYSITELIB}/cutadapt/parser.pyc
+${PYSITELIB}/cutadapt/pipeline.pyo
+${PYSITELIB}/cutadapt/pipeline.pyc
 ${PYSITELIB}/cutadapt/report.pyo
-${PYSITELIB}/cutadapt/scripts/__init__.py
-${PYSITELIB}/cutadapt/scripts/__init__.pyc
-${PYSITELIB}/cutadapt/scripts/__init__.pyo
-${PYSITELIB}/cutadapt/scripts/cutadapt.py
-${PYSITELIB}/cutadapt/scripts/cutadapt.pyc
-${PYSITELIB}/cutadapt/scripts/cutadapt.pyo
-${PYSITELIB}/cutadapt/seqio.py
-${PYSITELIB}/cutadapt/seqio.pyc
-${PYSITELIB}/cutadapt/seqio.pyo
+${PYSITELIB}/cutadapt/report.pyc
+${PYSITELIB}/cutadapt/utils.pyo
+${PYSITELIB}/cutadapt/utils.pyc
+${PYSITELIB}/cutadapt/_align.so
+${PYSITELIB}/cutadapt/_version.py
+${PYSITELIB}/cutadapt/adapters.py
+${PYSITELIB}/cutadapt/align.py
+${PYSITELIB}/cutadapt/filters.py
+${PYSITELIB}/cutadapt/log.py
+${PYSITELIB}/cutadapt/modifiers.py
+${PYSITELIB}/cutadapt/parser.py
+${PYSITELIB}/cutadapt/pipeline.py
+${PYSITELIB}/cutadapt/qualtrim.so
+${PYSITELIB}/cutadapt/report.py
+${PYSITELIB}/cutadapt/utils.py
diff --git a/py-cutadapt/distinfo b/py-cutadapt/distinfo
index 6d9b648a89..526724b8ec 100644
--- a/py-cutadapt/distinfo
+++ b/py-cutadapt/distinfo
@@ -1,6 +1,6 @@
 $NetBSD$
 
-SHA1 (cutadapt-1.14.tar.gz) = cffd036c46e1c159fee6b0da23b175499023de37
-RMD160 (cutadapt-1.14.tar.gz) = 591f69a597f04a04a09538cb67d832a838d5a404
-SHA512 (cutadapt-1.14.tar.gz) = 22028c586801293e1942525f343ee72e590f8a10a3244e9aaadaded45a6f4e126f66d0fd6a6aa821b70d36a9735b7cc74f6582f9fe13b6273387f9d917d55a43
-Size (cutadapt-1.14.tar.gz) = 283631 bytes
+SHA1 (cutadapt-2.5.tar.gz) = bc92e43825d5d10892b69cdbd21448f17353c477
+RMD160 (cutadapt-2.5.tar.gz) = dacb42583d0dea114b2bcf42ac7da9d2c79e3436
+SHA512 (cutadapt-2.5.tar.gz) = fa114dc4d8dfc03325c1bc8b41101aa1dfac7b3fbbf71d98bd3422cb054ae1b475e0cdc56519a49cba95e432d5fec3b8abe4f58b915ad487f335f0fd62994715
+Size (cutadapt-2.5.tar.gz) = 269321 bytes