[med-svn] [Git][med-team/python-xopen][master] 4 commits: routine-update: New upstream version
Nilesh Patra
gitlab at salsa.debian.org
Sun Jan 24 07:36:02 GMT 2021
Nilesh Patra pushed to branch master at Debian Med / python-xopen
Commits:
37fac3bd by Nilesh Patra at 2021-01-24T13:02:07+05:30
routine-update: New upstream version
- - - - -
a86084cc by Nilesh Patra at 2021-01-24T13:02:09+05:30
New upstream version 1.1.0
- - - - -
ebf04348 by Nilesh Patra at 2021-01-24T13:02:10+05:30
Update upstream source from tag 'upstream/1.1.0'
Update to upstream version '1.1.0'
with Debian dir 2317351aca3aa474465405735469d2e3b100901f
- - - - -
1bbe1f25 by Nilesh Patra at 2021-01-24T13:02:28+05:30
routine-update: Ready to upload to unstable
- - - - -
13 changed files:
- + .github/workflows/ci.yml
- − .travis.yml
- PKG-INFO
- README.rst
- debian/changelog
- setup.py
- src/xopen.egg-info/PKG-INFO
- src/xopen.egg-info/SOURCES.txt
- src/xopen.egg-info/requires.txt
- src/xopen/__init__.py
- src/xopen/_version.py
- tests/test_xopen.py
- tox.ini
Changes:
=====================================
.github/workflows/ci.yml
=====================================
@@ -0,0 +1,86 @@
+name: CI
+
+on: [push, pull_request]
+
+jobs:
+ lint:
+ timeout-minutes: 5
+ runs-on: ubuntu-latest
+ strategy:
+ matrix:
+ python-version: [3.7]
+ toxenv: [flake8, mypy]
+ steps:
+ - uses: actions/checkout at v2
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python at v2
+ with:
+ python-version: ${{ matrix.python-version }}
+ - name: Install dependencies
+ run: python -m pip install tox
+ - name: Run tox ${{ matrix.toxenv }}
+ run: tox -e ${{ matrix.toxenv }}
+
+ test:
+ timeout-minutes: 5
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ os: [ubuntu-latest]
+ python-version: [3.6, 3.7, 3.8, 3.9, pypy3]
+ include:
+ - os: macos-latest
+ python-version: 3.7
+ - os: ubuntu-20.04
+ python-version: 3.7
+ with-isal: true
+ steps:
+ - name: Install pigz
+ run: >
+ if [[ ${{ startsWith(matrix.os, 'macos') }} = true ]]; then
+ brew install pigz;
+ else
+ sudo apt-get install pigz;
+ fi
+ - name: Install isal
+ if: matrix.with-isal && !startsWith(matrix.os, 'macos')
+ run: sudo apt-get install isal libisal-dev
+ - uses: actions/checkout at v2
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python at v2
+ with:
+ python-version: ${{ matrix.python-version }}
+ - name: Install dependencies
+ run: python -m pip install tox
+ - name: Test
+ run: tox -e py
+ if: matrix.with-isal == null
+ - name: Test with isal
+ run: tox -e isal
+ if: matrix.with-isal
+ - name: Upload coverage report
+ uses: codecov/codecov-action at v1
+
+ deploy:
+ timeout-minutes: 5
+ runs-on: ubuntu-latest
+ needs: [lint, test]
+ if: startsWith(github.ref, 'refs/tags')
+ steps:
+ - uses: actions/checkout at v2
+ with:
+ fetch-depth: 0 # required for setuptools_scm
+ - name: Set up Python
+ uses: actions/setup-python at v2
+ with:
+ python-version: 3.7
+ - name: Make distributions
+ run: |
+ python setup.py sdist
+ python -m pip wheel --no-deps -w dist/ .
+ ls -l dist/
+ - name: Publish to PyPI
+ uses: pypa/gh-action-pypi-publish at v1.4.1
+ with:
+ user: __token__
+ password: ${{ secrets.pypi_password }}
=====================================
.travis.yml deleted
=====================================
@@ -1,67 +0,0 @@
-language: python
-
-dist: focal
-
-cache:
- directories:
- - $HOME/.cache/pip
-
-python:
- - "3.5"
- - "3.6"
- - "3.7"
- - "3.8"
- - "3.9"
- - "pypy3"
-
-install:
- - sudo apt-get update && sudo apt-get install -y pigz
- - pip install --upgrade coverage codecov
- - pip install .
-
-script:
- - python setup.py --version # Detect encoding problems
- - coverage run -m pytest
-
-after_success:
- - coverage combine
- - codecov
-
-env:
- global:
- - TWINE_USERNAME=marcelm
-
-jobs:
- include:
- - stage: deploy
- services:
- - docker
- python: "3.6"
- install: python3 -m pip install twine
- if: tag IS present
- script:
- - |
- python3 setup.py sdist
- python3 -m pip wheel -w dist/ .
- ls -l dist/
- python3 -m twine upload dist/xopen-*
-
- - stage: test
- name: flake8
- python: "3.6"
- install: python3 -m pip install flake8
- script: flake8 src/ tests/
-
- - stage: test
- name: mypy
- python: "3.6"
- install: python3 -m pip install mypy
- script: mypy src/
-
- - stage: test
- name: igzip
- python: "3.6"
- install:
- - sudo apt-get update && sudo apt-get install -y pigz isal
- - pip install --upgrade coverage codecov
- - pip install .
=====================================
PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 2.1
Name: xopen
-Version: 1.0.1
+Version: 1.1.0
Summary: Open compressed files transparently
Home-page: https://github.com/marcelm/xopen/
Author: Marcel Martin
@@ -38,12 +38,21 @@ Description: .. image:: https://travis-ci.org/marcelm/xopen.svg?branch=master
available. For gzip compression levels 1 to 3,
`igzip <https://github.com/intel/isa-l/>`_ is used for an even greater speedup.
+ For use cases where using only the main thread is desired xopen can be used
+ with ``threads=0``. This will use `python-isal
+ <https://github.com/pycompression/python-isal>`_ (which binds isa-l) if
+ python-isal is installed (automatic on Linux systems, as it is a requirement).
+ For installation instructions for python-isal please
+ checkout the `python-isal homepage
+ <https://github.com/pycompression/python-isal>`_. If python-isal is not
+ available ``gzip.open`` is used.
+
This module has originally been developed as part of the `Cutadapt
tool <https://cutadapt.readthedocs.io/>`_ that is used in bioinformatics to
manipulate sequencing data. It has been in successful use within that software
for a few years.
- ``xopen`` is compatible with Python versions 3.5 and later.
+ ``xopen`` is compatible with Python versions 3.6 and later.
Usage
@@ -94,6 +103,12 @@ Description: .. image:: https://travis-ci.org/marcelm/xopen.svg?branch=master
Changes
-------
+ v1.1.0
+ ~~~~~~
+ * Python 3.5 support is dropped.
+ * On Linux systems, `python-isal <https://github.com/pycompression/python-isal>`_
+ is now added as a requirement. This will speed up the reading of gzip files
+ significantly when no external processes are used.
v1.0.0
~~~~~~
@@ -162,5 +177,5 @@ Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
-Requires-Python: >=3.5
+Requires-Python: >=3.6
Provides-Extra: dev
=====================================
README.rst
=====================================
@@ -30,12 +30,21 @@ when reading ``.gz`` files, so it is used both for reading and writing if it is
available. For gzip compression levels 1 to 3,
`igzip <https://github.com/intel/isa-l/>`_ is used for an even greater speedup.
+For use cases where using only the main thread is desired xopen can be used
+with ``threads=0``. This will use `python-isal
+<https://github.com/pycompression/python-isal>`_ (which binds isa-l) if
+python-isal is installed (automatic on Linux systems, as it is a requirement).
+For installation instructions for python-isal please
+checkout the `python-isal homepage
+<https://github.com/pycompression/python-isal>`_. If python-isal is not
+available ``gzip.open`` is used.
+
This module has originally been developed as part of the `Cutadapt
tool <https://cutadapt.readthedocs.io/>`_ that is used in bioinformatics to
manipulate sequencing data. It has been in successful use within that software
for a few years.
-``xopen`` is compatible with Python versions 3.5 and later.
+``xopen`` is compatible with Python versions 3.6 and later.
Usage
@@ -86,6 +95,12 @@ If you also want to open S3 files, you may want to use that module instead.
Changes
-------
+v1.1.0
+~~~~~~
+* Python 3.5 support is dropped.
+* On Linux systems, `python-isal <https://github.com/pycompression/python-isal>`_
+ is now added as a requirement. This will speed up the reading of gzip files
+ significantly when no external processes are used.
v1.0.0
~~~~~~
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+python-xopen (1.1.0-1) unstable; urgency=medium
+
+ * New upstream version
+
+ -- Nilesh Patra <npatra974 at gmail.com> Sun, 24 Jan 2021 13:02:28 +0530
+
python-xopen (1.0.1-2) unstable; urgency=medium
* Clean _version.py pre-build
=====================================
setup.py
=====================================
@@ -19,8 +19,9 @@ setup(
package_data={"xopen": ["py.typed"]},
extras_require={
'dev': ['pytest'],
+ ':sys_platform=="linux" and python_implementation != "PyPy"': ['isal>=0.3.0']
},
- python_requires='>=3.5',
+ python_requires='>=3.6',
classifiers=[
"Development Status :: 5 - Production/Stable",
"License :: OSI Approved :: MIT License",
=====================================
src/xopen.egg-info/PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 2.1
Name: xopen
-Version: 1.0.1
+Version: 1.1.0
Summary: Open compressed files transparently
Home-page: https://github.com/marcelm/xopen/
Author: Marcel Martin
@@ -38,12 +38,21 @@ Description: .. image:: https://travis-ci.org/marcelm/xopen.svg?branch=master
available. For gzip compression levels 1 to 3,
`igzip <https://github.com/intel/isa-l/>`_ is used for an even greater speedup.
+ For use cases where using only the main thread is desired xopen can be used
+ with ``threads=0``. This will use `python-isal
+ <https://github.com/pycompression/python-isal>`_ (which binds isa-l) if
+ python-isal is installed (automatic on Linux systems, as it is a requirement).
+ For installation instructions for python-isal please
+ checkout the `python-isal homepage
+ <https://github.com/pycompression/python-isal>`_. If python-isal is not
+ available ``gzip.open`` is used.
+
This module has originally been developed as part of the `Cutadapt
tool <https://cutadapt.readthedocs.io/>`_ that is used in bioinformatics to
manipulate sequencing data. It has been in successful use within that software
for a few years.
- ``xopen`` is compatible with Python versions 3.5 and later.
+ ``xopen`` is compatible with Python versions 3.6 and later.
Usage
@@ -94,6 +103,12 @@ Description: .. image:: https://travis-ci.org/marcelm/xopen.svg?branch=master
Changes
-------
+ v1.1.0
+ ~~~~~~
+ * Python 3.5 support is dropped.
+ * On Linux systems, `python-isal <https://github.com/pycompression/python-isal>`_
+ is now added as a requirement. This will speed up the reading of gzip files
+ significantly when no external processes are used.
v1.0.0
~~~~~~
@@ -162,5 +177,5 @@ Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
-Requires-Python: >=3.5
+Requires-Python: >=3.6
Provides-Extra: dev
=====================================
src/xopen.egg-info/SOURCES.txt
=====================================
@@ -1,13 +1,13 @@
.codecov.yml
.editorconfig
.gitignore
-.travis.yml
LICENSE
README.rst
pyproject.toml
setup.cfg
setup.py
tox.ini
+.github/workflows/ci.yml
src/xopen/__init__.py
src/xopen/_version.py
src/xopen/_version.pyi
=====================================
src/xopen.egg-info/requires.txt
=====================================
@@ -1,3 +1,6 @@
+[:sys_platform=="linux" and python_implementation != "PyPy"]
+isal>=0.3.0
+
[dev]
pytest
=====================================
src/xopen/__init__.py
=====================================
@@ -27,6 +27,12 @@ try:
except ImportError:
lzma = None # type: ignore
+try:
+ from isal import igzip, isal_zlib # type: ignore
+except ImportError:
+ igzip = None
+ isal_zlib = None
+
try:
import fcntl
# fcntl.F_SETPIPE_SZ will be available in python 3.10.
@@ -470,31 +476,47 @@ def _open_xz(filename, mode: str) -> IO:
return lzma.open(filename, mode)
+def _open_gz_external(filename, mode, compresslevel, threads):
+ if 'r' in mode:
+ try:
+ return PipedIGzipReader(filename, mode)
+ except (OSError, ValueError):
+ # No igzip installed or version does not support reading
+ # concatenated files.
+ return PipedGzipReader(filename, mode, threads=threads)
+ else:
+ try:
+ return PipedIGzipWriter(filename, mode, compresslevel)
+ except (OSError, ValueError):
+ # No igzip installed or compression level higher than 3
+ return PipedGzipWriter(filename, mode, compresslevel,
+ threads=threads)
+
+
def _open_gz(filename, mode: str, compresslevel, threads):
if threads != 0:
try:
- if 'r' in mode:
- try:
- return PipedIGzipReader(filename, mode)
- except (OSError, ValueError):
- # No igzip installed or version does not support reading
- # concatenated files.
- return PipedGzipReader(filename, mode, threads=threads)
- else:
- try:
- return PipedIGzipWriter(filename, mode, compresslevel)
- except (OSError, ValueError):
- # No igzip installed or compression level higher than 3
- return PipedGzipWriter(filename, mode, compresslevel, threads=threads)
+ return _open_gz_external(filename, mode, compresslevel, threads)
except OSError:
pass # We try without threads.
if 'r' in mode:
+ if igzip is not None:
+ return igzip.open(filename, mode)
return gzip.open(filename, mode)
- else:
- # Override gzip.open's default of 9 for consistency with command-line gzip.
- return gzip.open(filename, mode,
- compresslevel=6 if compresslevel is None else compresslevel)
+
+ if igzip is not None:
+ try:
+ return igzip.open(filename, mode,
+ compresslevel=isal_zlib.ISAL_DEFAULT_COMPRESSION
+ if compresslevel is None else compresslevel)
+ except ValueError:
+ # Compression level not supported, move to built-in gzip.
+ pass
+
+ # Override gzip.open's default of 9 for consistency with command-line gzip.
+ return gzip.open(filename, mode,
+ compresslevel=6 if compresslevel is None else compresslevel)
def _detect_format_from_content(filename: str) -> Optional[str]:
=====================================
src/xopen/_version.py
=====================================
@@ -1,4 +1,5 @@
# coding: utf-8
# file generated by setuptools_scm
# don't change, don't track in version control
-version = '1.0.1'
+version = '1.1.0'
+version_tuple = (1, 1, 0)
=====================================
tests/test_xopen.py
=====================================
@@ -431,7 +431,7 @@ def test_concatenated_gzip_function():
@pytest.mark.skipif(
- not hasattr(fcntl, "F_GETPIPE_SZ") and _MAX_PIPE_SIZE is not None,
+ not hasattr(fcntl, "F_GETPIPE_SZ") or _MAX_PIPE_SIZE is None,
reason="Pipe size modifications not available on this platform.")
def test_pipesize_changed(tmpdir):
path = Path(str(tmpdir), "hello.gz")
=====================================
tox.ini
=====================================
@@ -1,20 +1,34 @@
[tox]
-envlist = flake8,mypy,py35,py36,py37,py38,py39,pypy3
+envlist = flake8,mypy,py36,py37,py38,py39,pypy3
[testenv]
-deps = pytest
+deps =
+ pytest
+ coverage
setenv = PYTHONDEVMODE = 1
-commands = pytest --doctest-modules --pyargs src/xopen tests
+commands =
+ coverage run --concurrency=multiprocessing -m pytest --doctest-modules src/xopen/ tests/
+ coverage combine
+ coverage report
+ coverage xml
+
+[testenv:isal]
+deps =
+ pytest
+ coverage
+ isal
[testenv:flake8]
basepython = python3.6
deps = flake8
commands = flake8 src/ tests/
+skip_install = true
[testenv:mypy]
basepython = python3.6
deps = mypy
commands = mypy src/
+skip_install = true
[flake8]
max-line-length = 99
View it on GitLab: https://salsa.debian.org/med-team/python-xopen/-/compare/2aa84eb8a3cc34a6ab150a05859f5966b506f04d...1bbe1f256131a9aca6f75d6438369c540acafd08
--
View it on GitLab: https://salsa.debian.org/med-team/python-xopen/-/compare/2aa84eb8a3cc34a6ab150a05859f5966b506f04d...1bbe1f256131a9aca6f75d6438369c540acafd08
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