CVS commit: pkgsrc/biology/py-cutadapt

["Adam Ciarcinski" <adam%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   adam
Date:           Mon Jan 17 09:03:10 UTC 2022

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

Log Message:
py-cutadapt: updated to 3.5

v3.5 (2021-09-29)
-----------------

* :issue:`555`: Add support for dumping statistics in JSON format using ``--json``.
* :issue:`541`: Add a "Read fate breakdown" section heading to the report, and also
  add statistics for reads discarded because of ``--discard-untrimmed`` and
  ``--discard-trimmed``. With this, the numbers in that section should add up to 100%.
* Add option ``-Q``, which allows to specify a quality-trimming threshold for R2 that is
  different from the one for R1.
* :issue:`567`: Add ``noindels`` adapter-trimming parameter. You can now write
  ``-a "ADAPTER;noindels"`` to disallow indels for a single adapter only.
* :issue:`570`: Fix ``--pair-adapters`` not finding some pairs when reads contain
  more than one adapter.
* :issue:`524`: Fix a memory leak when using ``--info-file`` with multiple cores.
* :issue:`559`: Fix adjacent base statistics not being shown for linked adapters.


To generate a diff of this commit:
cvs rdiff -u -r1.8 -r1.9 pkgsrc/biology/py-cutadapt/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/py-cutadapt/PLIST
cvs rdiff -u -r1.5 -r1.6 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/Makefile
diff -u pkgsrc/biology/py-cutadapt/Makefile:1.8 pkgsrc/biology/py-cutadapt/Makefile:1.9
--- pkgsrc/biology/py-cutadapt/Makefile:1.8     Wed Jan  5 15:40:57 2022
+++ pkgsrc/biology/py-cutadapt/Makefile Mon Jan 17 09:03:10 2022
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.8 2022/01/05 15:40:57 wiz Exp $
+# $NetBSD: Makefile,v 1.9 2022/01/17 09:03:10 adam Exp $
 
-DISTNAME=      cutadapt-3.4
+DISTNAME=      cutadapt-3.5
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
-PKGREVISION=   2
 CATEGORIES=    biology python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=c/cutadapt/}
 
@@ -12,11 +11,10 @@ COMMENT=    Find and remove adapter sequenc
 LICENSE=       mit
 
 TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools_scm-[0-9]*:../../devel/py-setuptools_scm
-
 DEPENDS+=      ${PYPKGPREFIX}-dnaio>=0.5.0:../../biology/py-dnaio
 DEPENDS+=      ${PYPKGPREFIX}-xopen>=1.0.0:../../devel/py-xopen
 
-PYTHON_VERSIONS_INCOMPATIBLE=  27 # py-xopen, dataclasses
+PYTHON_VERSIONS_INCOMPATIBLE=  27 # py-xopen
 
 USE_PKG_RESOURCES=     yes
 

Index: pkgsrc/biology/py-cutadapt/PLIST
diff -u pkgsrc/biology/py-cutadapt/PLIST:1.2 pkgsrc/biology/py-cutadapt/PLIST:1.3
--- pkgsrc/biology/py-cutadapt/PLIST:1.2        Thu Feb 11 10:30:55 2021
+++ pkgsrc/biology/py-cutadapt/PLIST    Mon Jan 17 09:03:10 2022
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.2 2021/02/11 10:30:55 adam Exp $
+@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
@@ -25,6 +25,9 @@ ${PYSITELIB}/cutadapt/align.pyo
 ${PYSITELIB}/cutadapt/filters.py
 ${PYSITELIB}/cutadapt/filters.pyc
 ${PYSITELIB}/cutadapt/filters.pyo
+${PYSITELIB}/cutadapt/json.py
+${PYSITELIB}/cutadapt/json.pyc
+${PYSITELIB}/cutadapt/json.pyo
 ${PYSITELIB}/cutadapt/log.py
 ${PYSITELIB}/cutadapt/log.pyc
 ${PYSITELIB}/cutadapt/log.pyo
@@ -41,6 +44,12 @@ ${PYSITELIB}/cutadapt/qualtrim.so
 ${PYSITELIB}/cutadapt/report.py
 ${PYSITELIB}/cutadapt/report.pyc
 ${PYSITELIB}/cutadapt/report.pyo
+${PYSITELIB}/cutadapt/statistics.py
+${PYSITELIB}/cutadapt/statistics.pyc
+${PYSITELIB}/cutadapt/statistics.pyo
+${PYSITELIB}/cutadapt/steps.py
+${PYSITELIB}/cutadapt/steps.pyc
+${PYSITELIB}/cutadapt/steps.pyo
 ${PYSITELIB}/cutadapt/tokenizer.py
 ${PYSITELIB}/cutadapt/tokenizer.pyc
 ${PYSITELIB}/cutadapt/tokenizer.pyo

Index: pkgsrc/biology/py-cutadapt/distinfo
diff -u pkgsrc/biology/py-cutadapt/distinfo:1.5 pkgsrc/biology/py-cutadapt/distinfo:1.6
--- pkgsrc/biology/py-cutadapt/distinfo:1.5     Tue Oct 26 10:03:43 2021
+++ pkgsrc/biology/py-cutadapt/distinfo Mon Jan 17 09:03:10 2022
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.5 2021/10/26 10:03:43 nia Exp $
+$NetBSD: distinfo,v 1.6 2022/01/17 09:03:10 adam Exp $
 
-BLAKE2s (cutadapt-3.4.tar.gz) = 0013ccc827e0082669442387094d30d78e32d01e3212e2b4d259ec3c006c4f17
-SHA512 (cutadapt-3.4.tar.gz) = 8d0556acb2c67146adf68eb208d2ec9701f391e6554d5e1ebaf146a12e3ba02c68b01856c254c94917ba9e919df26ece97a2c41ea386747e1c495eecbf4b2e0c
-Size (cutadapt-3.4.tar.gz) = 295282 bytes
+BLAKE2s (cutadapt-3.5.tar.gz) = acfca3b84b2ef7d1cf030b288dd4ea464f8c3243c1566a354f5113a92c2799a1
+SHA512 (cutadapt-3.5.tar.gz) = 7ffb2afc1fd57cd30c4c618db0c1c3dde3803bff19709b158537a46c50b4ddc367abf5707e876f139ba5ad1dc18122fa5b69a1db019c03ed7b605cfbb222ef66
+Size (cutadapt-3.5.tar.gz) = 303774 bytes