py-dnaio: Update to 0.5.0 py-cutadapt: Update to 3.2

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: py-dnaio: Update to 0.5.0 py-cutadapt: Update to 3.2
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Fri, 05 Feb 2021 22:18:43 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Feb 5 16:18:43 2021 -0600
Changeset:	47a15bf9ea8bcc371afb0f7c5796778cf7e888d4

Modified Files:
	py-cutadapt/Makefile
	py-cutadapt/PLIST
	py-cutadapt/distinfo
	py-dnaio/Makefile
	py-dnaio/distinfo
Removed Files:
	py-cutadapt/patches/patch-setup.py

Log Message:
py-dnaio: Update to 0.5.0
py-cutadapt: Update to 3.2

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=47a15bf9ea8bcc371afb0f7c5796778cf7e888d4

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

diffstat:
 py-cutadapt/Makefile               |  2 +-
 py-cutadapt/PLIST                  | 49 ++++++++++++++++++++------------------
 py-cutadapt/distinfo               |  9 ++++---
 py-cutadapt/patches/patch-setup.py | 15 ------------
 py-dnaio/Makefile                  |  6 ++---
 py-dnaio/distinfo                  |  8 +++----
 6 files changed, 37 insertions(+), 52 deletions(-)

diffs:
diff --git a/py-cutadapt/Makefile b/py-cutadapt/Makefile
index d17edf2462..1a63c4eba8 100644
--- a/py-cutadapt/Makefile
+++ b/py-cutadapt/Makefile
@@ -4,7 +4,7 @@
 #               Generated by fbsd2pkg                     #
 ###########################################################
 
-DISTNAME=	cutadapt-2.5
+DISTNAME=	cutadapt-3.2
 PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_PYPI:=c/cutadapt/}
diff --git a/py-cutadapt/PLIST b/py-cutadapt/PLIST
index f1052a859b..e58188d61d 100644
--- a/py-cutadapt/PLIST
+++ b/py-cutadapt/PLIST
@@ -7,40 +7,43 @@ ${PYSITELIB}/${EGG_INFODIR}/entry_points.txt
 ${PYSITELIB}/${EGG_INFODIR}/requires.txt
 ${PYSITELIB}/${EGG_INFODIR}/top_level.txt
 ${PYSITELIB}/cutadapt/__init__.py
-${PYSITELIB}/cutadapt/__main__.py
-${PYSITELIB}/cutadapt/__init__.pyo
 ${PYSITELIB}/cutadapt/__init__.pyc
-${PYSITELIB}/cutadapt/__main__.pyo
+${PYSITELIB}/cutadapt/__init__.pyo
+${PYSITELIB}/cutadapt/__main__.py
 ${PYSITELIB}/cutadapt/__main__.pyc
-${PYSITELIB}/cutadapt/_version.pyo
-${PYSITELIB}/cutadapt/_version.pyc
-${PYSITELIB}/cutadapt/adapters.pyo
-${PYSITELIB}/cutadapt/adapters.pyc
-${PYSITELIB}/cutadapt/align.pyo
-${PYSITELIB}/cutadapt/align.pyc
-${PYSITELIB}/cutadapt/filters.pyo
-${PYSITELIB}/cutadapt/filters.pyc
-${PYSITELIB}/cutadapt/log.pyo
-${PYSITELIB}/cutadapt/log.pyc
-${PYSITELIB}/cutadapt/modifiers.pyo
-${PYSITELIB}/cutadapt/modifiers.pyc
-${PYSITELIB}/cutadapt/parser.pyo
-${PYSITELIB}/cutadapt/parser.pyc
-${PYSITELIB}/cutadapt/pipeline.pyo
-${PYSITELIB}/cutadapt/pipeline.pyc
-${PYSITELIB}/cutadapt/report.pyo
-${PYSITELIB}/cutadapt/report.pyc
-${PYSITELIB}/cutadapt/utils.pyo
-${PYSITELIB}/cutadapt/utils.pyc
+${PYSITELIB}/cutadapt/__main__.pyo
 ${PYSITELIB}/cutadapt/_align.so
 ${PYSITELIB}/cutadapt/_version.py
+${PYSITELIB}/cutadapt/_version.pyc
+${PYSITELIB}/cutadapt/_version.pyo
 ${PYSITELIB}/cutadapt/adapters.py
+${PYSITELIB}/cutadapt/adapters.pyc
+${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
 ${PYSITELIB}/cutadapt/log.py
+${PYSITELIB}/cutadapt/log.pyc
+${PYSITELIB}/cutadapt/log.pyo
 ${PYSITELIB}/cutadapt/modifiers.py
+${PYSITELIB}/cutadapt/modifiers.pyc
+${PYSITELIB}/cutadapt/modifiers.pyo
 ${PYSITELIB}/cutadapt/parser.py
+${PYSITELIB}/cutadapt/parser.pyc
+${PYSITELIB}/cutadapt/parser.pyo
 ${PYSITELIB}/cutadapt/pipeline.py
+${PYSITELIB}/cutadapt/pipeline.pyc
+${PYSITELIB}/cutadapt/pipeline.pyo
 ${PYSITELIB}/cutadapt/qualtrim.so
 ${PYSITELIB}/cutadapt/report.py
+${PYSITELIB}/cutadapt/report.pyc
+${PYSITELIB}/cutadapt/report.pyo
+${PYSITELIB}/cutadapt/tokenizer.py
+${PYSITELIB}/cutadapt/tokenizer.pyc
+${PYSITELIB}/cutadapt/tokenizer.pyo
 ${PYSITELIB}/cutadapt/utils.py
+${PYSITELIB}/cutadapt/utils.pyc
+${PYSITELIB}/cutadapt/utils.pyo
diff --git a/py-cutadapt/distinfo b/py-cutadapt/distinfo
index af444fa587..86b4cfb88f 100644
--- a/py-cutadapt/distinfo
+++ b/py-cutadapt/distinfo
@@ -1,7 +1,6 @@
 $NetBSD$
 
-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
-SHA1 (patch-setup.py) = c1ddc55533acc8c21d929c5fd61c7f755028f130
+SHA1 (cutadapt-3.2.tar.gz) = 11b2545862c4e9a655a279f951b15558b1617506
+RMD160 (cutadapt-3.2.tar.gz) = e04f8be21e118c760dc03d80544c1d4f7135f985
+SHA512 (cutadapt-3.2.tar.gz) = 97ab1cadc3bd1585012c0aba916b0031d8b13bff1f1894f4548b6f7bfa20b5f2d598c499664d755a81be57e36fd5c712f36df77cfcd1f2b28a4f27990ee0b56c
+Size (cutadapt-3.2.tar.gz) = 292702 bytes
diff --git a/py-cutadapt/patches/patch-setup.py b/py-cutadapt/patches/patch-setup.py
deleted file mode 100644
index 19e5c9705e..0000000000
--- a/py-cutadapt/patches/patch-setup.py
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD$
-
-# Allow dnaio > 0.3
-
---- setup.py.orig	2019-10-10 20:20:05.117582567 +0000
-+++ setup.py
-@@ -102,7 +102,7 @@ setup(
-     package_dir={'': 'src'},
-     packages=find_packages('src'),
-     entry_points={'console_scripts': ['cutadapt = cutadapt.__main__:main']},
--    install_requires=['dnaio~=0.3.0', 'xopen~=0.8.1'],
-+    install_requires=['dnaio>=0.3.0', 'xopen>=0.8.1'],
-     extras_require={
-         'dev': ['Cython', 'pytest', 'pytest-timeout', 'sphinx', 'sphinx_issues'],
-     },
diff --git a/py-dnaio/Makefile b/py-dnaio/Makefile
index f2cb7aaf07..07bdab1af7 100644
--- a/py-dnaio/Makefile
+++ b/py-dnaio/Makefile
@@ -5,8 +5,8 @@
 #              Thu Oct 10 15:09:51 CDT 2019               #
 ###########################################################
 
-DISTNAME=	dnaio-${PV}
-PKGNAME=	${PYPKGPREFIX}-dnaio-${PV}
+DISTNAME=	dnaio-0.5.0
+PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_PYPI:=d/dnaio/}
 
@@ -22,8 +22,6 @@ LICENSE=	mit
 # Just assuming C and C++: Adjust this!
 USE_LANGUAGES=	c
 
-PV=		0.4
-
 # Verify that we shouldn't use distutils.mk or extensions.mk instead.
 .include "../../lang/python/egg.mk"
 # Based on USES=python.  Check this.
diff --git a/py-dnaio/distinfo b/py-dnaio/distinfo
index 76394fb855..4e2647fa01 100644
--- a/py-dnaio/distinfo
+++ b/py-dnaio/distinfo
@@ -1,6 +1,6 @@
 $NetBSD$
 
-SHA1 (dnaio-0.4.tar.gz) = f4073d7a3f032dbfaaf3bb05d94a68c2a6886118
-RMD160 (dnaio-0.4.tar.gz) = 5ae69f8146d86595a09714affe4d8d8cc75614a5
-SHA512 (dnaio-0.4.tar.gz) = e6491ceab5c810cfb06f807ac24cfe95f963323002344d37a17f6c60669139469c7a6ca4ddaf19dc37c3a20c7eea9bcd80c2fcfb6378ee4f1acd5540b032b084
-Size (dnaio-0.4.tar.gz) = 123137 bytes
+SHA1 (dnaio-0.5.0.tar.gz) = 466b533b83ef34baab0492199264a6d88d34be57
+RMD160 (dnaio-0.5.0.tar.gz) = 731c217d956cf03088851579bd364d510b8222ec
+SHA512 (dnaio-0.5.0.tar.gz) = 2e6a0dd04558b70ee08a81fd1d118525734df52701735cc27bab4c423c2030ec2fb6e83ddf02c491e1eb250c471d230b8fa72993c3a20ae844716c9542059c67
+Size (dnaio-0.5.0.tar.gz) = 126321 bytes
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