Fix build for Cython v3.0.0 #39

Workflow file for this run

	# Python: "3.8", "3.9", "3.10"
	# Older version do not support f-strings
	# OS: ubuntu-20.04, ubuntu-latest
	# OS: macOS-10.15, macos-11 (, macos-latest)
	# OS: windows-2019


	name: Python package

	on:
	push:
	branches: [ deploy ]
	pull_request:
	banches: [ deploy ]

	jobs:
	# Explore-GitHub-Actions:
	# runs-on: ubuntu-latest
	# steps:
	# - run: echo "🎉 The job was automatically triggered by a ${{ github.event_name }} event."
	# - run: echo "🐧 This job is now running on a ${{ runner.os }} server hosted by GitHub!"
	# - run: echo "🔎 The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}."
	# - name: Check out repository code
	# uses: actions/checkout@v2
	# - run: echo "💡 The ${{ github.repository }} repository has been cloned to the runner."
	# - run: echo "🖥️ The workflow is now ready to test your code on the runner."
	# - name: List files in the repository
	# run: \|
	# ls ${{ github.workspace }}
	# - run: echo "🍏 This job's status is ${{ job.status }}."

	# # Does not produce manylinux that is required for twine
	# build_unix:
	# name: Build wheels on ${{ matrix.os }}
	# runs-on: ${{ matrix.os }}
	# strategy:
	# fail-fast: true
	# matrix:
	# # os: [ubuntu-20.04,ubuntu-18.04]
	# # python-version: ["3.8","3.9","3.10"]
	# os: [ubuntu-18.04]
	# python-version: ["3.9"]
	# steps:
	# - uses: actions/checkout@v2
	# - name: Set up Python ${{ matrix.python-version }}
	# uses: actions/setup-python@v2
	# with:
	# python-version: ${{ matrix.python-version }}
	# - name: Install dependencies
	# run: \|
	# python -m pip install --upgrade pip
	# python -m pip install pytest pytest-benchmark build
	# python -m pip install numpy scipy matplotlib>=3.0.0
	# if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
	# - name: Compile and install
	# run: \|
	# python -m pip install . -v
	# ls ${{ github.workspace }}/build \|\| true
	# - name: Test installation
	# run : \|
	# mv dtaidistance dtaidistance_pkg
	# python ./util/check_installation.py
	# mv dtaidistance_pkg dtaidistance
	# - name: Test with pytest
	# run: \|
	# mv dtaidistance dtaidistance_pkg
	# pytest --ignore=venv --benchmark-skip
	# mv dtaidistance_pkg dtaidistance
	# - name: Build
	# run: \|
	# python -m build
	# - name: Store wheels
	# uses: actions/upload-artifact@v2
	# with:
	# name: wheels
	# path: dist/*.whl

	build_unix:
	name: Build wheels on ${{ matrix.os }}
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: true
	matrix:
	# os: [ubuntu-20.04,ubuntu-18.04]
	# python-version: ["3.8","3.9","3.10"]
	os: [ubuntu-18.04]
	# cibuildwheel will automatically provide all Python versions
	python-version: ["3.9"]
	steps:
	- uses: actions/checkout@v2
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	python -m pip install cibuildwheel==2.3.1
	- name: Build wheel
	run: \|
	pwd
	ls
	python -m cibuildwheel --output-dir dist/
	env:
	CIBW_BUILD_VERBOSITY: 2
	# cp36-* and cp37-* do not support f-strings
	CIBW_SKIP: cp36-* cp37-* pp* -manylinux_i686 -musllinux_i686 *-musllinux_x86_64
	CIBW_TEST_EXTRAS: "dev"
	CIBW_TEST_COMMAND: pytest --ignore=venv --benchmark-skip {project}/tests
	- name: Store wheels
	uses: actions/upload-artifact@v2
	with:
	name: wheels
	path: dist/*.whl


	build_macos:
	name: Build wheels on ${{ matrix.os }}
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: true
	matrix:
	os: [macos-11]
	python-version: ["3.8","3.9","3.10"]
	steps:
	- uses: actions/checkout@v2
	- name: Install OpenMP
	run: \|
	# OpenMP libraries are not installed by default on macos
	clang --version
	clang --version \| grep "13\."
	# hardcoded, not ideal
	# https://mac.r-project.org/openmp/
	curl -O https://mac.r-project.org/openmp/openmp-13.0.0-darwin21-Release.tar.gz
	sudo tar fvxz openmp-13.0.0-darwin21-Release.tar.gz -C /
	ls /usr/local/lib
	ls /usr/local/include
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	python -m pip install pytest pytest-benchmark build
	python -m pip install numpy scipy matplotlib>=3.0.0
	if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
	- name: Compile and install
	run: \|
	export LDFLAGS="-L/usr/local/lib"
	export CPPFLAGS="-I/usr/local/include"
	python -m pip install . -v
	ls ${{ github.workspace }}/build \|\| true
	- name: Test installation
	run : \|
	mv dtaidistance dtaidistance_pkg
	python ./util/check_installation.py
	mv dtaidistance_pkg dtaidistance
	- name: Test with pytest
	run: \|
	export LDFLAGS="-L/usr/local/lib"
	export CPPFLAGS="-I/usr/local/include"
	mv dtaidistance dtaidistance_pkg
	pytest --ignore=venv --benchmark-skip
	mv dtaidistance_pkg dtaidistance
	- name: Build
	run: \|
	python -m build
	- name: Store wheels
	uses: actions/upload-artifact@v2
	with:
	name: wheels
	path: dist/*.whl

	build_windows:
	name: Build wheels on ${{ matrix.os }}
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: true
	matrix:
	os: [windows-2019]
	python-version: ["3.8","3.9","3.10"]
	steps:
	- uses: actions/checkout@v2
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	python -m pip install pytest pytest-benchmark pytest-env build cython
	python -m pip install numpy scipy matplotlib>=3.0.0
	- name: Compile and install
	run: \|
	python -m pip install . -v
	ls ${{ github.workspace }}/build \|\| true
	- name: Test installation
	run : \|
	mv dtaidistance dtaidistance_pkg
	python ./util/check_installation.py
	mv dtaidistance_pkg dtaidistance
	- name: Test with pytest
	run: \|
	mv dtaidistance dtaidistance_pkg
	pytest --ignore=venv --benchmark-skip
	mv dtaidistance_pkg dtaidistance
	- name: Build
	run: \|
	python -m build
	- name: Store wheels
	uses: actions/upload-artifact@v2
	with:
	name: wheels
	path: dist/*.whl

	build_sdist:
	name: Prepare source distribution
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v1
	- name: Setup Python
	uses: actions/setup-python@v2
	with:
	python-version: '3.9'
	- name: Build
	run: \|
	python -m pip install build
	python -m build --sdist
	- name: Store artifacts
	uses: actions/upload-artifact@v2
	with:
	name: wheels
	path: dist/*.tar.gz


	upload_wheels:
	name: Upload wheels to PyPi
	runs-on: ubuntu-latest
	# upload to PyPI on every tag starting with 'v'
	# if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
	needs: [build_unix,build_macos,build_windows,build_sdist]

	steps:
	- uses: actions/download-artifact@v2
	with:
	name: wheels
	path: dist

	- name: Publish package to PyPI
	uses: pypa/gh-action-pypi-publish@release/v1
	with:
	user: __token__
	password: ${{ secrets.PYPI_API_TOKEN }}
	packages_dir: dist/

	# test_upload_wheels:
	# name: Upload wheels to TestPyPi
	# runs-on: ubuntu-latest
	# # upload to PyPI on every tag starting with 'v'
	# # if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
	# needs: [build_unix,build_macos,build_windows,build_sdist]
	# # needs: [build_unix]
	# steps:
	# - uses: actions/download-artifact@v2
	# with:
	# name: wheels
	# path: dist

	# - name: Publish package to TestPyPI
	# uses: pypa/gh-action-pypi-publish@release/v1
	# with:
	# user: __token__
	# password: ${{ secrets.TEST_PYPI_API_TOKEN_TEST }}
	# repository_url: https://test.pypi.org/legacy/

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Fix build for Cython v3.0.0 #39

Workflow file

Fix build for Cython v3.0.0 #39

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Workflow file for this run