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Fix issue where threads would block python exit when an error is thrown and the file cannot be closed. #824

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Fix issue where threads would block python exit when an error is thrown and the file cannot be closed.

Fix issue where threads would block python exit when an error is thrown and the file cannot be closed. #824

Workflow file for this run

.github/workflows/ci.yml at a0639b9
name: Continous integration
on:
pull_request:
push:
branches:
- develop
- main
tags:
- "*"
jobs:
lint:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
with:
submodules: recursive
- name: Set up Python 3.8
uses: actions/[email protected]
with:
python-version: 3.8
- name: Install tox
run: pip install tox
- name: Lint
run: tox -e lint
package-checks:
strategy:
matrix:
tox_env:
- docs
- twine_check
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
with:
submodules: recursive
- name: Set up Python 3.8
uses: actions/[email protected]
with:
python-version: 3.8
- name: Install isal
run: sudo apt-get install libisal-dev
- name: Install tox and upgrade setuptools and pip
run: pip install --upgrade tox setuptools pip
- name: Run tox -e ${{ matrix.tox_env }}
run: tox -e ${{ matrix.tox_env }}
env:
PYTHON_ISAL_LINK_DYNAMIC: True
test-static:
runs-on: ${{ matrix.os }}
strategy:
matrix:
python-version:
- "3.8"
- "3.9"
- "3.10"
- "3.11"
- "3.12"
- "3.13-dev"
- "pypy-3.9"
- "pypy-3.10"
os: ["ubuntu-latest"]
include:
- os: "macos-13"
python-version: "3.8"
- os: "macos-14"
python-version: "3.10"
- os: "windows-latest"
python-version: "3.8"
steps:
- uses: actions/checkout@v4
with:
submodules: recursive
- name: Set up Python ${{ matrix.python-version }}
uses: actions/[email protected]
with:
python-version: ${{ matrix.python-version }}
- name: Install tox and upgrade setuptools
run: pip install --upgrade tox setuptools
- name: Install build dependencies (Linux) # Yasm in pypa/manylinux images.
run: sudo apt install nasm
if: runner.os == 'Linux'
- name: Install build dependencies (Macos)
# Install yasm because nasm does not work when building wheels.
# Probably because of nasm-filter.sh not filtering all flags that can not be used.
run: brew install nasm
if: runner.os == 'macOS'
- name: Set MSVC developer prompt
uses: ilammy/[email protected]
if: runner.os == 'Windows'
- name: Install nasm (Windows)
uses: ilammy/[email protected]
if: runner.os == 'Windows'
- name: Run tests
run: tox
- name: Upload coverage report
uses: codecov/codecov-action@v1
test-arch:
if: startsWith(github.ref, 'refs/tags') || github.ref == 'refs/heads/develop' || github.ref == 'refs/heads/main'
runs-on: "ubuntu-latest"
strategy:
matrix:
python_version:
- "3.8"
steps:
- uses: actions/checkout@v4
with:
submodules: recursive
- uses: uraimo/[email protected]
name: Build & run test
with:
arch: none
distro: none
base_image: "--platform=linux/arm64 quay.io/pypa/manylinux2014_aarch64"
# versioningit needs an accessible git repository but the container
# is run as root, which is different from the repository user.
# use git config to override this.
run: |-
git config --global --add safe.directory $PWD
CFLAGS="-DNDEBUG -g0" python${{matrix.python_version}} -m pip install . pytest
python${{matrix.python_version}} -m pytest tests
# Test if the python-isal conda package can be build. Which is linked
# dynamically to the conda isa-l package.
test-dynamic:
runs-on: ${{ matrix.os }}
defaults:
run:
# This is needed for miniconda, see:
# https://github.com/marketplace/actions/setup-miniconda#important.
shell: bash -l {0}
strategy:
matrix:
os: ["ubuntu-latest", "macos-13", "windows-latest"]
python_version: [ "python" ]
include:
- os: "ubuntu-latest"
python_version: "pypy"
steps:
- uses: actions/checkout@v4
with:
submodules: recursive
- name: Install miniconda.
uses: conda-incubator/setup-miniconda@v3 # https://github.com/conda-incubator/setup-miniconda.
with:
channels: conda-forge,defaults
- name: Install requirements (universal)
run: conda install isa-l ${{ matrix.python_version}} tox
- name: Set MSVC developer prompt
uses: ilammy/[email protected]
if: runner.os == 'Windows'
- name: Run tests (dynamic link)
run: tox
env:
PYTHON_ISAL_LINK_DYNAMIC: True
deploy:
if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
runs-on: ${{ matrix.os }}
needs:
- lint
- package-checks
- test-static
- test-dynamic
- test-arch
strategy:
matrix:
os:
- ubuntu-latest
- macos-13
- macos-14
- windows-latest
cibw_archs_linux: ["x86_64"]
cibw_before_all_linux:
- >-
curl -o nasm-2.15.05.tar.gz https://www.nasm.us/pub/nasm/releasebuilds/2.15.05/nasm-2.15.05.tar.gz &&
tar -xzvf nasm-2.15.05.tar.gz &&
cd nasm-2.15.05/ &&
./autogen.sh &&
./configure &&
make nasm &&
install -c nasm /usr/bin/nasm
build_sdist: [true]
include:
- os: "ubuntu-latest"
cibw_archs_linux: "aarch64"
cibw_before_all_linux: "true" # The true command exits with 0
steps:
- uses: actions/checkout@v4
with:
submodules: recursive
fetch-depth: 0 # Fetch everything to get accurately versioned tag.
- uses: actions/setup-python@v2
name: Install Python
- name: Install cibuildwheel twine wheel
run: python -m pip install cibuildwheel twine wheel
- name: Install build dependencies (Macos)
run: brew install nasm
if: runner.os == 'macOS'
- name: Set MSVC developer prompt
uses: ilammy/[email protected]
if: runner.os == 'Windows'
- name: Install nasm (Windows)
uses: ilammy/[email protected]
if: runner.os == 'Windows'
- name: Set up QEMU
if: ${{runner.os == 'Linux' && matrix.cibw_archs_linux == 'aarch64'}}
uses: docker/[email protected]
with:
platforms: arm64
- name: Build wheels
run: cibuildwheel --output-dir dist
env:
CIBW_SKIP: "*-win32 *-manylinux_i686 cp38-macosx_*arm64 cp39-macosx_*arm64" # Skip 32 bit and problematic mac builds.
CIBW_ARCHS_LINUX: ${{ matrix.cibw_archs_linux }}
CIBW_BEFORE_ALL_LINUX: ${{ matrix.cibw_before_all_linux }}
# Fully test the build wheels again.
CIBW_TEST_REQUIRES: "pytest"
# Simple tests that requires the project to be build correctly
# Skip extensive compatibility testing which is slow.
CIBW_TEST_COMMAND_LINUX: >-
pytest -v {project}/tests/test_igzip.py
{project}/tests/test_gzip_compliance.py
{project}/tests/test_zlib_compliance.py
{project}/tests/test_igzip_lib.py
-k 'not test_compress_decompress'
CIBW_TEST_COMMAND_MACOS: >-
pytest -v {project}/tests/test_igzip.py
{project}/tests/test_gzip_compliance.py
{project}/tests/test_zlib_compliance.py
{project}/tests/test_igzip_lib.py
-k 'not test_compress_decompress'
# Windows does not have the test module apparently. Do more expensive
# tests to verify build.
CIBW_TEST_COMMAND_WINDOWS: >-
pytest {project}/tests/test_igzip.py
{project}/tests/test_igzip_lib.py
{project}/tests/test_compat.py
CIBW_ENVIRONMENT_LINUX: >-
PYTHON_ISAL_BUILD_CACHE=True
PYTHON_ISAL_BUILD_CACHE_FILE=/tmp/build_cache
CFLAGS="-g0 -DNDEBUG"
CIBW_ENVIRONMENT_WINDOWS: >-
PYTHON_ISAL_BUILD_CACHE=True
PYTHON_ISAL_BUILD_CACHE_FILE=${{ runner.temp }}\build_cache
CIBW_ENVIRONMENT_MACOS: >-
PYTHON_ISAL_BUILD_CACHE=True
PYTHON_ISAL_BUILD_CACHE_FILE=${{ runner.temp }}/build_cache
CFLAGS="-g0 -DNDEBUG"
- name: Build sdist
if: ${{runner.os == 'Linux' && matrix.cibw_archs_linux == 'x86_64'}}
run: |
pip install build
python -m build --sdist
- uses: actions/upload-artifact@v2
with:
name: "dist"
path: "dist/"
- name: Publish package to TestPyPI
# pypa/gh-action-pypi-publish@master does not work on OSX
# Alpha, Beta and dev releases contain a - in the tag.
if: contains(github.ref, '-') && startsWith(github.ref, 'refs/tags')
run: twine upload --skip-existing --repository-url https://test.pypi.org/legacy/ dist/*
env:
TWINE_USERNAME: __token__
TWINE_PASSWORD: ${{ secrets.TEST_PYPI_API_TOKEN }}
- name: Publish package to PyPI
if: "!contains(github.ref, '-') && startsWith(github.ref, 'refs/tags')"
run: twine upload --skip-existing dist/*
env:
TWINE_USERNAME: __token__
TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}