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[pkgsrc/trunk]: pkgsrc/biology/py-dnaio py-dnaio: update to 0.9.1.
details: https://anonhg.NetBSD.org/pkgsrc/rev/9c385d7a2b3c
branches: trunk
changeset: 388134:9c385d7a2b3c
user: wiz <wiz%pkgsrc.org@localhost>
date: Mon Nov 14 10:39:40 2022 +0000
description:
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
diffstat:
biology/py-dnaio/Makefile | 10 ++++------
biology/py-dnaio/PLIST | 14 +++++++++++++-
biology/py-dnaio/distinfo | 8 ++++----
3 files changed, 21 insertions(+), 11 deletions(-)
diffs (86 lines):
diff -r e3b12cab184b -r 9c385d7a2b3c biology/py-dnaio/Makefile
--- a/biology/py-dnaio/Makefile Mon Nov 14 10:35:15 2022 +0000
+++ b/biology/py-dnaio/Makefile Mon Nov 14 10:39:40 2022 +0000
@@ -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 @@
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"
diff -r e3b12cab184b -r 9c385d7a2b3c biology/py-dnaio/PLIST
--- a/biology/py-dnaio/PLIST Mon Nov 14 10:35:15 2022 +0000
+++ b/biology/py-dnaio/PLIST Mon Nov 14 10:39:40 2022 +0000
@@ -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}/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.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
${PYSITELIB}/dnaio/writers.pyo
diff -r e3b12cab184b -r 9c385d7a2b3c biology/py-dnaio/distinfo
--- a/biology/py-dnaio/distinfo Mon Nov 14 10:35:15 2022 +0000
+++ b/biology/py-dnaio/distinfo Mon Nov 14 10:39:40 2022 +0000
@@ -1,5 +1,5 @@
-$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
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