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Use cibuildwheel to build wheels for x86-64 and Aarch64
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@althonos
althonos committed Aug 16, 2023
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296 changes: 152 additions & 144 deletions .github/workflows/package.yml
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jobs:

wheel-linux:
runs-on: ubuntu-latest
name: Build Linux wheels
wheel-linux-aarch64:
name: Build Linux wheels (Aarch64)
runs-on: ubuntu-20.04
strategy:
matrix:
include:
- python-version: 3.6
pyo3-python: /opt/python/cp36-cp36m/bin/python
manylinux-img: quay.io/pypa/manylinux_2_24_x86_64
- python-version: 3.7
pyo3-python: /opt/python/cp37-cp37m/bin/python
manylinux-img: quay.io/pypa/manylinux_2_24_x86_64
- python-version: 3.8
pyo3-python: /opt/python/cp38-cp38/bin/python
manylinux-img: quay.io/pypa/manylinux_2_24_x86_64
- python-version: 3.9
pyo3-python: /opt/python/cp39-cp39/bin/python
manylinux-img: quay.io/pypa/manylinux_2_24_x86_64
- python-version: '3.10'
pyo3-python: /opt/python/cp310-cp310/bin/python
manylinux-img: quay.io/pypa/manylinux_2_24_x86_64
- python-version: '3.11'
pyo3-python: /opt/python/cp311-cp311/bin/python
manylinux-img: quay.io/pypa/manylinux_2_24_x86_64
- python-version: pypy-3.7
pyo3-python: /opt/python/pp37-pypy37_pp73/bin/python
manylinux-img: quay.io/pypa/manylinux_2_24_x86_64
- python-version: pypy-3.8
pyo3-python: /opt/python/pp38-pypy38_pp73/bin/python
manylinux-img: quay.io/pypa/manylinux_2_24_x86_64
- python-version: pypy-3.9
pyo3-python: /opt/python/pp39-pypy39_pp73/bin/python
manylinux-img: quay.io/pypa/manylinux_2_24_x86_64
python-tag:
- cp36-manylinux_aarch64
- cp37-manylinux_aarch64
- cp38-manylinux_aarch64
- cp39-manylinux_aarch64
- cp310-manylinux_aarch64
- cp311-manylinux_aarch64
- pp37-manylinux_aarch64
- pp38-manylinux_aarch64
- pp39-manylinux_aarch64
steps:
- name: Checkout code
uses: actions/checkout@v2
- uses: actions/checkout@v3
with:
submodules: true
- name: Set up QEMU
id: qemu
uses: docker/setup-qemu-action@v2
with:
platforms: all
- name: Build manylinux wheels
uses: addnab/docker-run-action@v2
uses: pypa/cibuildwheel@v2.11.3
env:
CIBW_ARCHS: aarch64
CIBW_BUILD: ${{ matrix.python-tag }}
CIBW_BUILD_VERBOSITY: 2
CIBW_BEFORE_BUILD: pip install cython
CIBW_TEST_COMMAND: python -m unittest pyhmmer.tests -vv
CIBW_TEST_REQUIRES: importlib-resources
with:
image: ${{ matrix.manylinux-img }}
options: -v ${{ github.workspace }}:/io -e TERM=$TERM
shell: bash
run: |
${{ matrix.pyo3-python }} -m pip install -U -r /io/.github/workflows/requirements.txt
${{ matrix.pyo3-python }} -m pip wheel --no-deps -vv /io -w /tmp
for whl in /tmp/*.whl; do ${{ matrix.pyo3-python }} -m auditwheel repair $whl -w /io/dist; done
- name: Store built wheels
uses: actions/upload-artifact@v2
output-dir: dist
- uses: actions/upload-artifact@v3
with:
name: dist
name: wheels
path: dist/*

test-linux:
runs-on: ubuntu-latest
name: Test Linux wheels
needs:
- wheel-linux
wheel-linux-x86_64:
name: Build Linux wheels (x86-64)
runs-on: ubuntu-20.04
strategy:
matrix:
python-version:
- 3.7
- 3.8
- 3.9
- '3.10'
- '3.11'
python-tag:
- cp36-manylinux_x86_64
- cp37-manylinux_x86_64
- cp38-manylinux_x86_64
- cp39-manylinux_x86_64
- cp310-manylinux_x86_64
- cp311-manylinux_x86_64
- pp37-manylinux_x86_64
- pp38-manylinux_x86_64
- pp39-manylinux_x86_64
steps:
- name: Setup Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
- uses: actions/checkout@v3
with:
python-version: ${{ matrix.python-version }}
- name: Download built wheels
uses: actions/download-artifact@v2
submodules: true
- uses: actions-rs/toolchain@v1
with:
name: dist
path: dist
- name: Update pip to latest version
run: python -m pip install -U pip setuptools wheel
- name: Install requirements
run: python -m pip install psutil
- name: Install built wheel
run: python -m pip install --no-index --find-links=dist pyhmmer
- name: Run tests without coverage
run: python -m unittest pyhmmer.tests -vv
toolchain: stable
override: true
- name: Build manylinux wheels
uses: pypa/cibuildwheel@v2.11.3
env:
CIBW_ARCHS: x86_64
CIBW_BUILD: ${{ matrix.python-tag }}
CIBW_BEFORE_BUILD: pip install cython
CIBW_BUILD_VERBOSITY: 2
CIBW_TEST_COMMAND: python -m unittest pyhmmer.tests -vv
CIBW_TEST_REQUIRES: importlib-resources
with:
output-dir: dist
- uses: actions/upload-artifact@v3
with:
name: wheels
path: dist/*

wheel-osx:
runs-on: macos-latest
name: Build OSX wheels
wheel-macos-x86_64:
name: Build MacOS wheels (x86-64)
runs-on: macOS-11
strategy:
matrix:
python-version:
- 3.7
- 3.8
- 3.9
- '3.10'
- '3.11'
- pypy-3.7
- pypy-3.8
- pypy-3.9
python-tag:
- cp36-macosx_x86_64
- cp37-macosx_x86_64
- cp38-macosx_x86_64
- cp39-macosx_x86_64
- cp310-macosx_x86_64
- cp311-macosx_x86_64
- pp37-macosx_x86_64
- pp38-macosx_x86_64
- pp39-macosx_x86_64
steps:
- name: Checkout code
uses: actions/checkout@v2
- uses: actions/checkout@v3
with:
submodules: true
- name: Cache Python requirements
uses: actions/cache@v2
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ matrix.python-version }}
restore-keys: |
${{ runner.os }}-pip-
- name: Cache built C files
uses: actions/cache@v2
- uses: actions-rs/toolchain@v1
with:
path: build
key: ${{ runner.os }}-build-${{ hashFiles('Prodigal/*') }}
restore-keys: |
${{ runner.os }}-build-
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
toolchain: stable
override: true
- name: Build manylinux wheels
uses: pypa/cibuildwheel@v2.11.3
env:
CIBW_ARCHS: x86_64
CIBW_BUILD: ${{ matrix.python-tag }}
CIBW_BEFORE_BUILD: pip install cython
CIBW_BUILD_VERBOSITY: 2
CIBW_TEST_COMMAND: python -m unittest pyhmmer.tests -vv
CIBW_TEST_REQUIRES: importlib-resources
with:
python-version: ${{ matrix.python-version }}
- name: Install Python requirements
run: python -m pip install -r .github/workflows/requirements.txt
- name: Build wheel distribution
run: python setup.py bdist_wheel
- name: Store built wheels
uses: actions/upload-artifact@v2
output-dir: dist
- uses: actions/upload-artifact@v3
with:
name: dist
name: wheels
path: dist/*

test-osx:
runs-on: macos-latest
name: Test OSX wheels
needs:
- wheel-osx
wheel-macos-aarch64:
name: Build MacOS wheels (Aarch64)
runs-on: macOS-11
strategy:
matrix:
python-version:
- 3.7
- 3.8
- 3.9
- '3.10'
- '3.11'
- pypy-3.7
- pypy-3.8
- pypy-3.9
python-tag:
- cp38-macosx_arm64
- cp39-macosx_arm64
- cp310-macosx_arm64
- cp311-macosx_arm64
steps:
- name: Setup Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
- uses: actions/checkout@v3
with:
python-version: ${{ matrix.python-version }}
- name: Download built wheels
uses: actions/download-artifact@v2
submodules: true
- uses: actions-rs/toolchain@v1
with:
name: dist
path: dist
- name: Update pip to latest version
run: python -m pip install -U pip setuptools wheel
- name: Install requirements
run: python -m pip install psutil
- name: Install built wheel
run: python -m pip install --no-index --find-links=dist pyhmmer
- name: Run tests without coverage
run: python -m unittest pyhmmer.tests -vv
toolchain: stable
override: true
target: aarch64-apple-darwin
- name: Build manylinux wheels
uses: pypa/cibuildwheel@v2.11.3
env:
CIBW_ARCHS: arm64
CIBW_BUILD: ${{ matrix.python-tag }}
CIBW_BEFORE_BUILD: pip install cython
CIBW_BUILD_VERBOSITY: 2
CIBW_TEST_COMMAND: python -m unittest pyhmmer.tests -vv
CIBW_TEST_REQUIRES: importlib-resources
with:
output-dir: dist
- uses: actions/upload-artifact@v3
with:
name: wheels
path: dist/*

sdist:
runs-on: ubuntu-latest
Expand All @@ -183,35 +168,58 @@ jobs:
uses: actions/checkout@v2
with:
submodules: true
- name: Set up Python 3.9
- name: Set up Python 3.11
uses: actions/setup-python@v2
with:
python-version: 3.9
python-version: 3.11
- name: Install build requirements
run: python -m pip install -r .github/workflows/requirements.txt
- name: Build wheel distribution
run: python setup.py sdist
- name: Store built wheels
uses: actions/upload-artifact@v2
with:
name: dist
name: wheels
path: dist/*

test-sdist:
runs-on: ubuntu-latest
name: Test source distribution
needs:
- sdist
steps:
- name: Setup Python 3.11
uses: actions/setup-python@v2
with:
python-version: '3.11'
- name: Download built wheels
uses: actions/download-artifact@v2
with:
name: wheels
path: dist/
- name: Update pip to latest version
run: python -m pip install -U pip setuptools wheel
- name: Install built wheel
run: python -m pip install --no-binary pyhmmer --find-links=dist pyhmmer
- name: Run tests without coverage
run: python -m unittest pyhmmer.tests -vv

upload:
environment: PyPI
runs-on: ubuntu-latest
name: Upload
needs:
- sdist
- wheel-linux
- test-linux
- wheel-osx
- test-osx
- test-sdist
- wheel-linux-aarch64
- wheel-linux-x86_64
- wheel-macos-x86_64
- wheel-macos-aarch64
steps:
- name: Download built distributions
uses: actions/download-artifact@v2
with:
name: dist
name: wheels
path: dist
- name: Publish distributions to PyPI
if: startsWith(github.ref, 'refs/tags/v')
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