[med-svn] [Git][med-team/python-dnaio][master] 5 commits: New upstream version 0.5.2
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Tue Sep 21 16:33:38 BST 2021
Nilesh Patra pushed to branch master at Debian Med / python-dnaio
Commits:
cff60c89 by Nilesh Patra at 2021-09-21T20:59:22+05:30
New upstream version 0.5.2
- - - - -
256f4403 by Nilesh Patra at 2021-09-21T20:59:22+05:30
routine-update: New upstream version
- - - - -
07078841 by Nilesh Patra at 2021-09-21T20:59:23+05:30
Update upstream source from tag 'upstream/0.5.2'
Update to upstream version '0.5.2'
with Debian dir 971057091861f6f99f0802031f315a7029e406de
- - - - -
2baa191b by Nilesh Patra at 2021-09-21T20:59:23+05:30
routine-update: Standards-Version: 4.6.0
- - - - -
aeeb6df0 by Nilesh Patra at 2021-09-21T20:59:30+05:30
routine-update: Ready to upload to unstable
- - - - -
7 changed files:
- .github/workflows/ci.yml
- + CHANGES.rst
- − buildwheels.sh
- debian/changelog
- debian/control
- src/dnaio/_core.pyx
- tests/test_internal.py
Changes:
=====================================
.github/workflows/ci.yml
=====================================
@@ -53,15 +53,22 @@ jobs:
- uses: actions/checkout at v2
with:
fetch-depth: 0 # required for setuptools_scm
+ - name: Build wheels
+ uses: pypa/cibuildwheel at v2.1.1
+ with:
+ output-dir: dist/
+ env:
+ CIBW_BUILD: "cp3*-manylinux_x86_64"
+ CIBW_MANYLINUX_X86_64_IMAGE: manylinux2010
+ CIBW_ENVIRONMENT: "CFLAGS=-g0"
- name: Set up Python
uses: actions/setup-python at v2
with:
python-version: 3.7
- name: Make distributions
run: |
- python -m pip install Cython
- python setup.py sdist
- ./buildwheels.sh
+ python -m pip install build
+ python -m build --sdist
ls -l dist/
- name: Publish to PyPI
uses: pypa/gh-action-pypi-publish at v1.4.1
=====================================
CHANGES.rst
=====================================
@@ -0,0 +1,8 @@
+=========
+Changelog
+=========
+
+v0.5.2 (2021-09-07)
+-------------------
+
+* Issue #7: Ignore a trailing "3" in the read id
=====================================
buildwheels.sh deleted
=====================================
@@ -1,47 +0,0 @@
-#!/bin/bash
-#
-# Build manylinux wheels. Based on the example at
-# <https://github.com/pypa/python-manylinux-demo>
-#
-# It is best to run this in a fresh clone of the repository!
-#
-# Run this within the repository root:
-# ./buildwheels.sh
-#
-# The wheels will be put into the dist/ subdirectory.
-
-set -xeuo pipefail
-
-manylinux=quay.io/pypa/manylinux2010_x86_64
-
-# For convenience, if this script is called from outside of a docker container,
-# it starts a container and runs itself inside of it.
-if ! grep -q docker /proc/1/cgroup && ! test -d /opt/python; then
- # We are not inside a container
- docker pull ${manylinux}
- exec docker run --rm -v $(pwd):/io ${manylinux} /io/$0
-fi
-
-if ! test -d /io/dist; then
- mkdir /io/dist
- chown --reference=/io/setup.py /io/dist
-fi
-
-# Strip binaries (copied from multibuild)
-STRIP_FLAGS=${STRIP_FLAGS:-"-Wl,-strip-all"}
-export CFLAGS="${CFLAGS:-$STRIP_FLAGS}"
-export CXXFLAGS="${CXXFLAGS:-$STRIP_FLAGS}"
-
-for PYBIN in /opt/python/cp3[6789]-*/bin; do
- ${PYBIN}/pip wheel --no-deps /io/ -w wheelhouse/
-done
-ls wheelhouse/
-
-# Bundle external shared libraries into the wheels
-for whl in wheelhouse/*.whl; do
- auditwheel repair "$whl" --plat manylinux1_x86_64 -w repaired/
-done
-
-# Created files are owned by root, so fix permissions.
-chown -R --reference=/io/setup.py repaired/
-mv repaired/*.whl /io/dist/
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+python-dnaio (0.5.2-1) unstable; urgency=medium
+
+ * New upstream version
+ * Standards-Version: 4.6.0 (routine-update)
+
+ -- Nilesh Patra <nilesh at debian.org> Tue, 21 Sep 2021 20:59:30 +0530
+
python-dnaio (0.5.1-1) unstable; urgency=medium
* d/watch: Fix watch regex
=====================================
debian/control
=====================================
@@ -11,7 +11,7 @@ Build-Depends: debhelper-compat (= 13),
python3-pytest,
python3-xopen,
cython3
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/python-dnaio
Vcs-Git: https://salsa.debian.org/med-team/python-dnaio.git
Homepage: https://github.com/marcelm/dnaio
=====================================
src/dnaio/_core.pyx
=====================================
@@ -297,16 +297,17 @@ def fastq_iter(file, sequence_class, Py_ssize_t buffer_size):
def record_names_match(header1: str, header2: str):
"""
Check whether the sequence record ids id1 and id2 are compatible, ignoring a
- suffix of '1' or '2'. Some old paired-end reads have names that end in '/1'
- and '/2'. Also, the fastq-dump tool (used for converting SRA files to FASTQ)
- appends a .1 and .2 to paired-end reads if option -I is used.
+ suffix of '1', '2' or '3'. This exception allows to check some old
+ paired-end reads that have names ending in '/1' and '/2'. Also, the
+ fastq-dump tool (used for converting SRA files to FASTQ) appends '.1', '.2'
+ and sometimes '.3' to paired-end reads if option -I is used.
"""
- # TODO optimize this a bit more
cdef:
str name1, name2
+
name1 = header1.split()[0]
name2 = header2.split()[0]
- if name1[-1:] in '12' and name2[-1:] in '12':
+ if name1 and name2 and name1[-1] in '123' and name2[-1] in '123':
name1 = name1[:-1]
name2 = name2[:-1]
return name1 == name2
=====================================
tests/test_internal.py
=====================================
@@ -470,10 +470,30 @@ class TestPairedSequenceReader:
def test_record_names_match(self):
match = record_names_match
assert match('abc', 'abc')
+ assert match('abc def', 'abc')
+ assert match('abc def', 'abc ghi')
+ assert match('abc', 'abc ghi')
+ assert not match('abc', 'xyz')
+
+ def test_record_names_match_with_ignored_trailing_12(self):
+ match = record_names_match
assert match('abc/1', 'abc/2')
assert match('abc.1', 'abc.2')
assert match('abc1', 'abc2')
- assert not match('abc', 'xyz')
+ assert match('abc2', 'abc1')
+ assert match('abc1 def', 'abc1 ghi')
+ assert match('abc1 def', 'abc2 ghi')
+ assert match('abc2 def', 'abc1 ghi')
+ assert not match('abc1', 'abc4')
+ assert not match('abc1', 'abc')
+ assert not match('abc', 'abc1')
+ assert not match('abc', 'abc2')
+
+ def test_record_names_match_with_ignored_trailing_123(self):
+ match = record_names_match
+ assert match('abc/1', 'abc/3')
+ assert match('abc.1 def', 'abc.3 ghi')
+ assert match('abc.3 def', 'abc.1 ghi')
def test_missing_partner1(self):
s1 = BytesIO(b'')
View it on GitLab: https://salsa.debian.org/med-team/python-dnaio/-/compare/0f4b6130c619d3c41209596da5af7c68d3b81921...aeeb6df0df3a28e91b83dea851f92237238435b4
--
View it on GitLab: https://salsa.debian.org/med-team/python-dnaio/-/compare/0f4b6130c619d3c41209596da5af7c68d3b81921...aeeb6df0df3a28e91b83dea851f92237238435b4
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