[med-svn] [Git][med-team/python-dnaio][master] 7 commits: New upstream version 0.4.3
Nilesh Patra
gitlab at salsa.debian.org
Sun Nov 8 07:51:07 GMT 2020
Nilesh Patra pushed to branch master at Debian Med / python-dnaio
Commits:
f3055552 by Nilesh Patra at 2020-11-08T13:16:36+05:30
New upstream version 0.4.3
- - - - -
a1d0cd67 by Nilesh Patra at 2020-11-08T13:16:36+05:30
routine-update: New upstream version
- - - - -
c7221d91 by Nilesh Patra at 2020-11-08T13:16:37+05:30
Update upstream source from tag 'upstream/0.4.3'
Update to upstream version '0.4.3'
with Debian dir 0cd5fa37daaeeae9703cfd3100be5f334edb71c4
- - - - -
03bfad40 by Nilesh Patra at 2020-11-08T13:16:37+05:30
routine-update: debhelper-compat 13
- - - - -
23da0ea6 by Nilesh Patra at 2020-11-08T13:16:47+05:30
routine-update: Add salsa-ci file
- - - - -
02c36867 by Nilesh Patra at 2020-11-08T13:16:51+05:30
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
- - - - -
ea207028 by Nilesh Patra at 2020-11-08T13:16:52+05:30
routine-update: Ready to upload to unstable
- - - - -
14 changed files:
- .travis.yml
- README.md
- buildwheels.sh
- debian/changelog
- debian/control
- + debian/salsa-ci.yml
- debian/upstream/metadata
- setup.py
- src/dnaio/__init__.py
- src/dnaio/readers.py
- src/dnaio/writers.py
- tests/test_internal.py
- tests/test_open.py
- tox.ini
Changes:
=====================================
.travis.yml
=====================================
@@ -7,7 +7,6 @@ cache:
- $HOME/.cache/pip
python:
- - "3.4"
- "3.5"
- "3.6"
- "3.7"
=====================================
README.md
=====================================
@@ -4,7 +4,7 @@
# dnaio parses FASTQ and FASTA
-`dnaio` is a Python 3 library for fast parsing of FASTQ and also FASTA files. The code was previously part of the
+`dnaio` is a Python 3.5+ library for fast parsing of FASTQ and also FASTA files. The code was previously part of the
[Cutadapt](https://cutadapt.readthedocs.io/) tool and has been improved since it has been split out.
=====================================
buildwheels.sh
=====================================
@@ -1,19 +1,30 @@
#!/bin/bash
#
-# Build manylinux1 wheels. Based on the example at
+# Build manylinux wheels. Based on the example at
# <https://github.com/pypa/python-manylinux-demo>
#
-# For interactive tests:
-# docker run -it -v $(pwd):/io quay.io/pypa/manylinux1_x86_64 /bin/bash
+# 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; then
# We are not inside a container
- docker pull quay.io/pypa/manylinux1_x86_64
- exec docker run --rm -v $(pwd):/io quay.io/pypa/manylinux1_x86_64 /io/$0
+ docker pull ${manylinux}
+ exec docker run --rm -v $(pwd):/io ${manylinux} /io/$0
+fi
+
+if ! test -d /io/dist; then
+ mkdir /io/dist
+ chown --reference=/io/setup.py /io/dist
fi
# Strip binaries (copied from multibuild)
@@ -21,21 +32,14 @@ STRIP_FLAGS=${STRIP_FLAGS:-"-Wl,-strip-all"}
export CFLAGS="${CFLAGS:-$STRIP_FLAGS}"
export CXXFLAGS="${CXXFLAGS:-$STRIP_FLAGS}"
-
-# We don’t support Python 2.7
-rm /opt/python/cp27*
-
-PYBINS="/opt/python/*/bin"
-HAS_CYTHON=0
-for PYBIN in ${PYBINS}; do
- ${PYBIN}/pip install Cython
-# ${PYBIN}/pip install -r /io/requirements.txt
- ${PYBIN}/pip wheel /io/ -w wheelhouse/
+for PYBIN in /opt/python/cp3[5678]-*/bin; do
+ ${PYBIN}/pip wheel --no-deps /io/ -w wheelhouse/
done
+ls wheelhouse/
# Bundle external shared libraries into the wheels
-for whl in wheelhouse/dnaio-*.whl; do
- auditwheel repair "$whl" -w repaired/
+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.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+python-dnaio (0.4.3-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * debhelper-compat 13 (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+ Repository-Browse.
+
+ -- Nilesh Patra <npatra974 at gmail.com> Sun, 08 Nov 2020 13:16:52 +0530
+
python-dnaio (0.4.2-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Liubov Chuprikova <chuprikovalv at gmail.com>
Section: python
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
dh-python,
python3-all-dev,
python3-setuptools,
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/upstream/metadata
=====================================
@@ -1,4 +1,6 @@
-Repository: https://github.com/marcelm/dnaio
+Bug-Database: https://github.com/marcelm/dnaio/issues
+Bug-Submit: https://github.com/marcelm/dnaio/issues/new
+Repository: https://github.com/marcelm/dnaio.git
Registry:
- Name: conda:bioconda
Entry: dnaio
@@ -6,3 +8,4 @@ Registry:
Entry: NA
- Name: OMICtools
Entry: NA
+Repository-Browse: https://github.com/marcelm/dnaio
=====================================
setup.py
=====================================
@@ -4,8 +4,8 @@ from setuptools import setup, Extension, find_packages
from distutils.command.sdist import sdist as _sdist
from distutils.command.build_ext import build_ext as _build_ext
-if sys.version_info[:2] < (3, 4):
- sys.stdout.write('Python 3.4 or later is required\n')
+if sys.version_info[:2] < (3, 5):
+ sys.stdout.write('Python 3.5 or later is required\n')
sys.exit(1)
@@ -75,9 +75,9 @@ setup(
ext_modules=extensions,
cmdclass={'build_ext': BuildExt, 'sdist': SDist},
install_requires=['xopen>=0.8.2'],
- python_requires='>=3.4',
+ python_requires='>=3.5',
classifiers=[
- "Development Status :: 4 - Beta",
+ "Development Status :: 5 - Production/Stable",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Natural Language :: English",
=====================================
src/dnaio/__init__.py
=====================================
@@ -128,6 +128,21 @@ def _detect_format_from_name(name):
return None
+def _is_path(obj):
+ """
+ Return whether the given object looks like a path (str, pathlib.Path or pathlib2.Path)
+ """
+ # pytest uses pathlib2.Path objects on Python 3.5 for its tmp_path fixture.
+ # On Python 3.6+, this function can be replaced with isinstance(obj, os.PathLike)
+ import sys
+ if "pathlib2" in sys.modules:
+ import pathlib2
+ path_classes = (str, pathlib.Path, pathlib2.Path)
+ else:
+ path_classes = (str, pathlib.Path)
+ return isinstance(obj, path_classes)
+
+
def _open_single(file, opener, *, fileformat=None, mode="r", qualities=None):
"""
Open a single sequence file. See description of open() above.
@@ -135,7 +150,7 @@ def _open_single(file, opener, *, fileformat=None, mode="r", qualities=None):
if mode not in ("r", "w", "a"):
raise ValueError("Mode must be 'r', 'w' or 'a'")
- if isinstance(file, (str, pathlib.Path)): # TODO Use os.PathLike in Python 3.6+
+ if _is_path(file):
path = fspath(file)
file = opener(path, mode + "b")
close_file = True
@@ -200,7 +215,8 @@ def _detect_format_from_content(file):
"""
if file.seekable():
first_char = file.read(1)
- file.seek(-1, 1)
+ if file.tell() > 0:
+ file.seek(-1, 1)
else:
first_char = file.peek(1)[0:1]
formats = {
@@ -228,6 +244,9 @@ class PairedSequenceReader:
self._close = stack.pop_all().close
self.delivers_qualities = self.reader1.delivers_qualities
+ def __repr__(self):
+ return "PairedSequenceReader(file1={}, file2={})".format(self.reader1, self.reader2)
+
def __iter__(self):
"""
Iterate over the paired reads. Each item is a pair of Sequence objects.
@@ -279,6 +298,9 @@ class InterleavedSequenceReader:
self.reader = _open_single(file, opener=opener, fileformat=fileformat)
self.delivers_qualities = self.reader.delivers_qualities
+ def __repr__(self):
+ return "InterleavedSequenceReader({})".format(self.reader)
+
def __iter__(self):
it = iter(self.reader)
for r1 in it:
@@ -317,6 +339,9 @@ class PairedSequenceWriter:
file2, opener=opener, fileformat=fileformat, mode=self._mode, qualities=qualities))
self._close = stack.pop_all().close
+ def __repr__(self):
+ return "{}({}, {})".format(self.__class__.__name__, self._writer1, self._writer2)
+
def write(self, read1, read2):
self._writer1.write(read1)
self._writer2.write(read2)
@@ -347,6 +372,9 @@ class InterleavedSequenceWriter:
self._writer = _open_single(
file, opener=opener, fileformat=fileformat, mode=self._mode, qualities=qualities)
+ def __repr__(self):
+ return "{}({})".format(self.__class__.__name__, self._writer)
+
def write(self, read1, read2):
self._writer.write(read1)
self._writer.write(read2)
=====================================
src/dnaio/readers.py
=====================================
@@ -30,6 +30,9 @@ class BinaryFileReader:
self._close_on_exit = True
self._file = file
+ def __repr__(self):
+ return "{}({!r})".format(self.__class__.__name__, getattr(self._file, "name", self._file))
+
def close(self):
if self._close_on_exit and self._file is not None:
self._file.close()
=====================================
src/dnaio/writers.py
=====================================
@@ -10,6 +10,9 @@ class FileWriter:
else:
self._close_on_exit = bool(_close_file)
+ def __repr__(self):
+ return "{}({!r})".format(self.__class__.__name__, getattr(self._file, "name", self._file))
+
def close(self):
if self._close_on_exit:
self._file.close()
@@ -36,6 +39,9 @@ class FastaWriter(FileWriter):
super().__init__(file, opener=opener, _close_file=_close_file)
self.line_length = line_length if line_length != 0 else None
+ def __repr__(self):
+ return "FastaWriter({!r})".format(getattr(self._file, "name", self._file))
+
def write(self, name_or_record, sequence=None):
"""Write an entry to the the FASTA file.
=====================================
tests/test_internal.py
=====================================
@@ -324,8 +324,6 @@ class TestInterleavedReader:
]
with InterleavedSequenceReader("tests/data/interleaved.fastq") as isr:
reads = list(isr)
- for (r1, r2), (e1, e2) in zip(reads, expected):
- print(r1, r2, e1, e2)
assert reads == expected
with dnaio.open("tests/data/interleaved.fastq", interleaved=True) as f:
=====================================
tests/test_open.py
=====================================
@@ -49,6 +49,20 @@ def test_version():
_ = dnaio.__version__
+def test_open_nonexistent(tmp_path):
+ with pytest.raises(FileNotFoundError):
+ with dnaio.open(tmp_path / "nonexistent"):
+ pass
+
+
+def test_open_empty_file_with_unrecognized_extension(tmp_path):
+ path = tmp_path / "unrecognized-extension.tmp"
+ path.touch()
+ with dnaio.open(path) as f:
+ records = list(f)
+ assert records == []
+
+
def test_read(fileformat, extension):
with dnaio.open("tests/data/simple." + fileformat + extension) as f:
records = list(f)
=====================================
tox.ini
=====================================
@@ -1,5 +1,5 @@
[tox]
-envlist = flake8,py34,py35,py36,py37,py38
+envlist = flake8,py35,py36,py37,py38
[testenv]
deps =
View it on GitLab: https://salsa.debian.org/med-team/python-dnaio/-/compare/351a8370a891d0a21add3d0786644731b5d0e6ef...ea2070280126b12a9e6b2454c12b9a7dc5a5eb9a
--
View it on GitLab: https://salsa.debian.org/med-team/python-dnaio/-/compare/351a8370a891d0a21add3d0786644731b5d0e6ef...ea2070280126b12a9e6b2454c12b9a7dc5a5eb9a
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