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Merge pull request #66 from larsoner/cbw
ENH: Add cibuildwheel and automated PyPI release
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‎.github/workflows/cibuildwheel.yml‎

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# Build wheels, sdist, and upload to PyPI
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# code adapted from antio and openmeeg
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# TODO: once numpy 1 support is dropped, enable these jobs; set to only run on
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# tagged releases, and only if the test.yml workflow is successful
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name: Build
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concurrency:
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group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
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cancel-in-progress: true
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on: # yamllint disable-line rule:truthy
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workflow_dispatch:
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release:
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types: [published]
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jobs:
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build_wheels:
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if: false # disabeling until we can drop support for numpy 1
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name: Wheels ${{ matrix.os }} ${{ matrix.arch }}
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-22.04, ubuntu-24.04, macos-14, macos-15, macos-15-intel] # windows-11 windows-11-arm
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arch: [native]
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# TODO: Someday this can be enabled, but need to add emulation and it's slow,
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# can use docker/setup-qemu-action
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# include:
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# - os: ubuntu-latest
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# arch: aarch64
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fail-fast: false
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steps:
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- uses: actions/checkout@v5
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- uses: pypa/cibuildwheel@v3.2.0
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with:
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output-dir: wheelhouse
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env:
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CIBW_ARCHS: ${{ matrix.arch }}
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- uses: actions/upload-artifact@v4
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with:
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name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
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path: ./wheelhouse/*.whl
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sdist:
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timeout-minutes: 10
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name: Create sdist
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: astral-sh/setup-uv@v6
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- run: uv build --sdist
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- uses: actions/upload-artifact@v4
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with:
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name: cibw-wheels-sdist
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path: ./dist/*.tar.gz
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check:
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needs: [build_wheels, sdist]
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timeout-minutes: 10
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name: run twine check
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5
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- uses: actions/download-artifact@v5
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with:
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pattern: cibw-wheels-*
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merge-multiple: true
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path: dist
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- run: ls -alt . && ls -alt dist/
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- uses: astral-sh/setup-uv@v6
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with:
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activate-environment: true
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- run: uv pip install twine -q --upgrade
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- run: twine check --strict dist/*
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publish:
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if: ${{ github.repository == 'freesurfer/surfa' && github.event_name == 'release' }}
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needs: [check]
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name: publish PyPI
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runs-on: ubuntu-latest
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permissions:
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id-token: write
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environment:
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name: pypi
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url: https://pypi.org/p/surfa
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timeout-minutes: 10
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steps:
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- uses: actions/download-artifact@v5
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with:
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pattern: cibw-wheels-*
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merge-multiple: true
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path: dist
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- uses: pypa/gh-action-pypi-publish@release/v1
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- uses: softprops/action-gh-release@v2
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with:
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files: dist/*
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tag_name: ${{ github.event.release.tag_name }}

‎.github/workflows/test.yml‎

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name: Package Test
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on: [push]
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on:
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push:
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pull_request:
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jobs:
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build-linux:
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runs-on: ubuntu-latest
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test:
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runs-on: ${{ matrix.os }}
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strategy:
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max-parallel: 5
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fail-fast: false
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matrix:
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os: [ubuntu-22.04, ubuntu-24.04, macos-14, macos-15, macos-15-intel]
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python-version: ['3.8', '3.9', '3.10', '3.11']
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Set up Python 3.8
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uses: actions/setup-python@v3
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: 3.8
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python-version: ${{ matrix.python-version }}
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- name: Display python and system info
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run: |
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python -c "import sys; print(f'python {sys.version}')"
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python -c "import platform; print(f'platform {platform.machine()}')"
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- name: Install package
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run: pip install .
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# need the -e flag so pytest can report coverage
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run: pip install -e .
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- name: Import test
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# simple test for now checking whether general import works
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run : python -c "import surfa; print('surfa imported successfully')"
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- name: Run tests
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working-directory: test
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#working-directory: test
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# simple test for now checking whether general import works
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# we should soon get some actual pytest scripts running
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run: python -c 'import surfa'
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run: |
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pip install pytest pytest-cov
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if [ -d "test" ]; then
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pytest --cov=surfa --cov-report=term -v
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else
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echo "No test directory, skipping"
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fi
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shell: bash

‎.gitignore‎

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docs/.deps
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docs/build
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docs/reference/api
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/wheelhouse
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.coverage

‎pyproject.toml‎

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[build-system]
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requires = ['setuptools', 'wheel', 'Cython>=3.0', 'numpy']
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[tool.cibuildwheel]
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build = ["cp3{8,9,10,11}-*"]
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archs = "native"
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before-build = "pip install abi3audit"
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test-command = "python -c \"import surfa; print(surfa.__version__)\""
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[tool.cibuildwheel.linux]
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repair-wheel-command = [
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"auditwheel repair -w {dest_dir} {wheel}",
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"bash tools/audit_wheel.sh {wheel}",
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]
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[tool.cibuildwheel.macos]
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archs = ["native"]
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repair-wheel-command = [
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"delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}",
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"bash tools/audit_wheel.sh {wheel}",
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]
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[tool.cibuildwheel.windows]
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before-build = "pip install delvewheel abi3audit"
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repair-wheel-command = [
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"delvewheel repair -w {dest_dir} {wheel}",
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"bash tools/audit_wheel.sh {wheel}",
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]

‎setup.py‎

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import re
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import pathlib
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import platform
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import sys
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from setuptools import setup
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from setuptools import dist
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from setuptools.extension import Extension
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from wheel.bdist_wheel import bdist_wheel
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# https://github.com/joerick/python-abi3-package-sample/blob/main/setup.py
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class bdist_wheel_abi3(bdist_wheel): # noqa: D101
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def get_tag(self): # noqa: D102
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python, abi, plat = super().get_tag()
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if python.startswith("cp"):
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return "cp311", "abi3", plat
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return python, abi, plat
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requirements = [
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base_dir = pathlib.Path(__file__).parent.resolve()
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# configure c extensions
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ext_opts = dict(extra_compile_args=['-O3', '-std=c99'])
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ext_opts = dict(
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extra_compile_args=['-O3', '-std=c99'],
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define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
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)
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macros = []
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setup_opts = {}
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if sys.version_info.minor >= 11 and platform.python_implementation() == "CPython":
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# Can create an abi3 wheel (typed memoryviews first available in 3.11)!
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ext_opts["define_macros"].append(("Py_LIMITED_API", "0x030B0000"))
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ext_opts["py_limited_api"] = True
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setup_opts["cmdclass"] = {"bdist_wheel": bdist_wheel_abi3}
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extensions = [
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Extension('surfa.image.interp', [f'surfa/image/interp.pyx'], **ext_opts),
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Extension('surfa.mesh.intersection', [f'surfa/mesh/intersection.pyx'], **ext_opts),
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]
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from Cython.Build import cythonize
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extensions = cythonize(extensions, compiler_directives={'language_level' : '3'})
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# since we interface the c stuff with numpy, it's another hard
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# requirement at build-time
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import numpy as np
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author='Andrew Hoopes',
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author_email='freesurfer@nmr.mgh.harvard.edu',
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url='https://github.com/freesurfer/surfa',
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python_requires='>=3.6',
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python_requires='>=3.8',
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packages=packages,
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ext_modules=extensions,
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include_dirs=include_dirs,
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'Natural Language :: English',
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'Topic :: Scientific/Engineering',
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],
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**setup_opts,
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)

‎tools/audit_wheel.sh‎

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#!/bin/bash -eo pipefail
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set -x
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PY_MINOR=$(python -c "import sys; print(sys.version_info.minor)")
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if [ "$PY_MINOR" -lt 11 ]; then
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echo "Not checking abi3audit for Python $PY_MINOR < 3.11"
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exit 0
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fi
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abi3audit --strict --report --verbose "$1"

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