CVS commit: pkgsrc/biology/py-dnaio

["Thomas Klausner" <wiz%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   wiz
Date:           Mon Nov 14 10:39:40 UTC 2022

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

Log Message:
py-dnaio: update to 0.9.1.

v0.9.1 (2022-08-01)
-------------------

* :pr:`85`: macOS wheels are now also built as part of the release procedure.
* :pr:`81`: API documentation improvements and minor code refactors for
  readability.

v0.9.0 (2022-05-17)
-------------------

* :pr:`79`: Added a `records_are_mates` function to be used for checking whether
  three or more records are mates of each other (by checking the ID).
* :pr:`74`, :pr:`68`: Made FASTQ parsing faster by implementing the check for
  ASCII using SSE vector instructions.
* :pr:`72`: Added a `tutorial <https://dnaio.readthedocs.io/en/latest/tutorial.html>`_.

v0.8.0 (2022-03-26)
-------------------

* Preliminary documentation is available at
  <https://dnaio.readthedocs.io/>.
* :pr:`53`: Renamed ``Sequence`` to `SequenceRecord`.
  The previous name is still available as an alias
  so that existing code will continue to work.
* When reading a FASTQ file, there is now a check that ensures that
  all characters are ASCII.
* Function ``record_names_match`` is deprecated, use `SequenceRecord.is_mate` instead.
* Dropped Python 3.6 support as it is end-of-life.

v0.7.1 (2022-01-26)
-------------------

* :pr:`34`: Fix parsing of FASTA files that just contain a comment and no reads

v0.7.0 (2022-01-17)
-------------------

* @rhpvorderman contributed many performance improvements in :pr:`15`,
  :pr:`17`, :pr:`18`, :pr:`20`, :pr:`21`, :pr:`22`, :pr:`23`. Reading
  and writing FASTQ files and reading of paired-end FASTQ files was
  sped up significantly. For example, reading uncompressed FASTQ is
  50% faster (!) than before.
* :pr:`28`: Windows support added

v0.6.0 (2021-09-28)
-------------------

* :pr:`12`: Improve FASTQ writing speed twofold (thanks to @rhpvorderman)

v0.5.2 (2021-09-07)
-------------------

* :issue:`7`: Ignore a trailing "3" in the read id


To generate a diff of this commit:
cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/py-dnaio/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/py-dnaio/PLIST
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/py-dnaio/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-dnaio/Makefile
diff -u pkgsrc/biology/py-dnaio/Makefile:1.6 pkgsrc/biology/py-dnaio/Makefile:1.7
--- pkgsrc/biology/py-dnaio/Makefile:1.6        Tue Jan  4 20:52:35 2022
+++ pkgsrc/biology/py-dnaio/Makefile    Mon Nov 14 10:39:40 2022
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.6 2022/01/04 20:52:35 wiz Exp $
+# $NetBSD: Makefile,v 1.7 2022/11/14 10:39:40 wiz Exp $
 
-DISTNAME=      dnaio-0.5.1
+DISTNAME=      dnaio-0.9.1
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
-PKGREVISION=   1
 CATEGORIES=    biology python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=d/dnaio/}
 
@@ -11,11 +10,10 @@ HOMEPAGE=   https://github.com/marcelm/dna
 COMMENT=       Read and write FASTQ and FASTA files
 LICENSE=       mit
 
-BUILD_DEPENDS+=        ${PYPKGPREFIX}-setuptools_scm-[0-9]*:../../devel/py-setuptools_scm
+TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools_scm-[0-9]*:../../devel/py-setuptools_scm
+TOOL_DEPENDS+= ${PYPKGPREFIX}-cython>=0.29.20:../../devel/py-cython
 DEPENDS+=      ${PYPKGPREFIX}-xopen>=0.8.2:../../devel/py-xopen
 
-# py-xopen and
-# "TypeError: 'encoding' is an invalid keyword argument for this function"
 PYTHON_VERSIONS_INCOMPATIBLE=  27
 
 .include "../../lang/python/egg.mk"

Index: pkgsrc/biology/py-dnaio/PLIST
diff -u pkgsrc/biology/py-dnaio/PLIST:1.2 pkgsrc/biology/py-dnaio/PLIST:1.3
--- pkgsrc/biology/py-dnaio/PLIST:1.2   Fri May 21 11:38:13 2021
+++ pkgsrc/biology/py-dnaio/PLIST       Mon Nov 14 10:39:40 2022
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.2 2021/05/21 11:38:13 adam Exp $
+@comment $NetBSD: PLIST,v 1.3 2022/11/14 10:39:40 wiz Exp $
 ${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
 ${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
 ${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
@@ -7,6 +7,7 @@ ${PYSITELIB}/${EGG_INFODIR}/top_level.tx
 ${PYSITELIB}/dnaio/__init__.py
 ${PYSITELIB}/dnaio/__init__.pyc
 ${PYSITELIB}/dnaio/__init__.pyo
+${PYSITELIB}/dnaio/_conversions.h
 ${PYSITELIB}/dnaio/_core.pyi
 ${PYSITELIB}/dnaio/_core.so
 ${PYSITELIB}/dnaio/_util.py
@@ -16,16 +17,27 @@ ${PYSITELIB}/dnaio/_version.py
 ${PYSITELIB}/dnaio/_version.pyc
 ${PYSITELIB}/dnaio/_version.pyi
 ${PYSITELIB}/dnaio/_version.pyo
+${PYSITELIB}/dnaio/ascii_check.h
+${PYSITELIB}/dnaio/ascii_check_sse2.h
 ${PYSITELIB}/dnaio/chunks.py
 ${PYSITELIB}/dnaio/chunks.pyc
 ${PYSITELIB}/dnaio/chunks.pyo
 ${PYSITELIB}/dnaio/exceptions.py
 ${PYSITELIB}/dnaio/exceptions.pyc
 ${PYSITELIB}/dnaio/exceptions.pyo
+${PYSITELIB}/dnaio/interfaces.py
+${PYSITELIB}/dnaio/interfaces.pyc
+${PYSITELIB}/dnaio/interfaces.pyo
+${PYSITELIB}/dnaio/pairedend.py
+${PYSITELIB}/dnaio/pairedend.pyc
+${PYSITELIB}/dnaio/pairedend.pyo
 ${PYSITELIB}/dnaio/py.typed
 ${PYSITELIB}/dnaio/readers.py
 ${PYSITELIB}/dnaio/readers.pyc
 ${PYSITELIB}/dnaio/readers.pyo
+${PYSITELIB}/dnaio/singleend.py
+${PYSITELIB}/dnaio/singleend.pyc
+${PYSITELIB}/dnaio/singleend.pyo
 ${PYSITELIB}/dnaio/writers.py
 ${PYSITELIB}/dnaio/writers.pyc
 ${PYSITELIB}/dnaio/writers.pyo

Index: pkgsrc/biology/py-dnaio/distinfo
diff -u pkgsrc/biology/py-dnaio/distinfo:1.4 pkgsrc/biology/py-dnaio/distinfo:1.5
--- pkgsrc/biology/py-dnaio/distinfo:1.4        Tue Oct 26 10:03:43 2021
+++ pkgsrc/biology/py-dnaio/distinfo    Mon Nov 14 10:39:40 2022
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.4 2021/10/26 10:03:43 nia Exp $
+$NetBSD: distinfo,v 1.5 2022/11/14 10:39:40 wiz Exp $
 
-BLAKE2s (dnaio-0.5.1.tar.gz) = 9eb6348e5dc2dacc625a8d005c929c312bca78ff7ca063573c1c3a55b8f599fc
-SHA512 (dnaio-0.5.1.tar.gz) = 127e3dcc8291c21e8adce71211692e9c2284d49df336bb923c53fc5fea7dcb9d9b9f047f95642f3300240dac3d43cf6e987b3148b4ffa239d70f3b6c7ef043a5
-Size (dnaio-0.5.1.tar.gz) = 126820 bytes
+BLAKE2s (dnaio-0.9.1.tar.gz) = 7c5ec560b4efba83d73bbcfdbfcd582b38e118f84e58dcd1701b0e63af314a2b
+SHA512 (dnaio-0.9.1.tar.gz) = c5975451fd458030a2626e4e85607232c7d169a4b6dabe88830006eea326a810c77955e7d104d30ddd4af5fe552fc10c292ef475a74f84d7e9f03bd9164b1993
+Size (dnaio-0.9.1.tar.gz) = 41594 bytes