ENH: Add cibuildwheel and automated PyPI release

.github/workflows/cibuildwheel.yml

@@ -0,0 +1,97 @@
+# Build wheels, sdist, and upload to PyPI
+
+# code adapted from antio and openmeeg
+# TODO: once numpy 1 support is dropped, enable these jobs; set to only run on
+# tagged releases, and only if the test.yml workflow is successful 
+
+name: Build
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:  # yamllint disable-line rule:truthy
+  workflow_dispatch:
+  release:
+    types: [published]
+
+jobs:
+  build_wheels:
+    if: false # disabeling until we can drop support for numpy 1
+    name: Wheels ${{ matrix.os }} ${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-22.04, ubuntu-24.04, macos-14, macos-15, macos-15-intel]  # windows-11 windows-11-arm
+        arch: [native]
+        # TODO: Someday this can be enabled, but need to add emulation and it's slow,
+        # can use docker/setup-qemu-action
+        # include:
+        #   - os: ubuntu-latest
+        #     arch: aarch64
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v5
+      - uses: pypa/cibuildwheel@v3.2.0
+        with:
+          output-dir: wheelhouse
+        env:
+          CIBW_ARCHS: ${{ matrix.arch }}
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  sdist:
+    timeout-minutes: 10
+    name: Create sdist
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v6
+      - run: uv build --sdist
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-sdist
+          path: ./dist/*.tar.gz
+
+  check:
+    needs: [build_wheels, sdist]
+    timeout-minutes: 10
+    name: run twine check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - uses: actions/download-artifact@v5
+        with:
+          pattern: cibw-wheels-*
+          merge-multiple: true
+          path: dist
+      - run: ls -alt . && ls -alt dist/
+      - uses: astral-sh/setup-uv@v6
+        with:
+          activate-environment: true
+      - run: uv pip install twine -q --upgrade
+      - run: twine check --strict dist/*
+
+  publish:
+    if: ${{ github.repository == 'freesurfer/surfa' && github.event_name == 'release' }}
+    needs: [check]
+    name: publish PyPI
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    environment:
+      name: pypi
+      url: https://pypi.org/p/surfa
+    timeout-minutes: 10
+    steps:
+      - uses: actions/download-artifact@v5
+        with:
+          pattern: cibw-wheels-*
+          merge-multiple: true
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1
+      - uses: softprops/action-gh-release@v2
+        with:
+          files: dist/*
+          tag_name: ${{ github.event.release.tag_name }}

.github/workflows/test.yml

@@ -1,26 +1,49 @@
 name: Package Test
 
-on: [push]
+on:
+  push:
+  pull_request:
 
 jobs:
-  build-linux:
-    runs-on: ubuntu-latest
+  test:
+    runs-on: ${{ matrix.os }}
     strategy:
       max-parallel: 5
+      fail-fast: false
+      matrix:
+        os: [ubuntu-22.04, ubuntu-24.04, macos-14, macos-15, macos-15-intel]
+        python-version: ['3.8', '3.9', '3.10', '3.11']
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v3
+    - name: Set up Python
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: ${{ matrix.python-version }}
+
+    - name: Display python and system info
+      run: |
+        python -c "import sys; print(f'python {sys.version}')"
+        python -c "import platform; print(f'platform {platform.machine()}')"
 
     - name: Install package
-      run: pip install .
+      # need the -e flag so pytest can report coverage
+      run: pip install -e .
+
+    - name: Import test
+      # simple test for now checking whether general import works
+      run : python -c "import surfa; print('surfa imported successfully')"
 
     - name: Run tests
-      working-directory: test
+      #working-directory: test
       # simple test for now checking whether general import works
       # we should soon get some actual pytest scripts running
-      run: python -c 'import surfa'
+      run: |
+        pip install pytest pytest-cov
+        if [ -d "test" ]; then
+          pytest --cov=surfa --cov-report=term -v
+        else
+          echo "No test directory, skipping"
+        fi
+      shell: bash

.gitignore

@@ -13,3 +13,6 @@ surfa.egg-info
 docs/.deps
 docs/build
 docs/reference/api
+/wheelhouse
+
+.coverage

pyproject.toml

@@ -1,2 +1,28 @@
 [build-system]
 requires = ['setuptools', 'wheel', 'Cython>=3.0', 'numpy']
+
+[tool.cibuildwheel]
+build = ["cp3{8,9,10,11}-*"]
+archs = "native"
+before-build = "pip install abi3audit"
+test-command = "python -c \"import surfa; print(surfa.__version__)\""
+
+[tool.cibuildwheel.linux]
+repair-wheel-command = [
+  "auditwheel repair -w {dest_dir} {wheel}",
+  "bash tools/audit_wheel.sh {wheel}",
+]
+
+[tool.cibuildwheel.macos]
+archs = ["native"]
+repair-wheel-command = [
+  "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}",
+  "bash tools/audit_wheel.sh {wheel}",
+]
+
+[tool.cibuildwheel.windows]
+before-build = "pip install delvewheel abi3audit"
+repair-wheel-command = [
+  "delvewheel repair -w {dest_dir} {wheel}",
+  "bash tools/audit_wheel.sh {wheel}",
+]

setup.py

@@ -2,10 +2,24 @@
 
 import re
 import pathlib
+import platform
+import sys
 
 from setuptools import setup
 from setuptools import dist
 from setuptools.extension import Extension
+from wheel.bdist_wheel import bdist_wheel
+
+
+# https://github.com/joerick/python-abi3-package-sample/blob/main/setup.py
+class bdist_wheel_abi3(bdist_wheel):  # noqa: D101
+    def get_tag(self):  # noqa: D102
+        python, abi, plat = super().get_tag()
+
+        if python.startswith("cp"):
+            return "cp311", "abi3", plat
+
+        return python, abi, plat
 
 
 requirements = [
@@ -30,15 +44,22 @@
 base_dir = pathlib.Path(__file__).parent.resolve()
 
 # configure c extensions
-ext_opts = dict(extra_compile_args=['-O3', '-std=c99'])
+ext_opts = dict(
+    extra_compile_args=['-O3', '-std=c99'],
+    define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
+)
+macros = []
+setup_opts = {}
+if sys.version_info.minor >= 11 and platform.python_implementation() == "CPython":
+    # Can create an abi3 wheel (typed memoryviews first available in 3.11)!
+    ext_opts["define_macros"].append(("Py_LIMITED_API", "0x030B0000"))
+    ext_opts["py_limited_api"] = True
+    setup_opts["cmdclass"] = {"bdist_wheel": bdist_wheel_abi3}
 extensions = [
     Extension('surfa.image.interp', [f'surfa/image/interp.pyx'], **ext_opts),
     Extension('surfa.mesh.intersection', [f'surfa/mesh/intersection.pyx'], **ext_opts),
 ]
 
-from Cython.Build import cythonize
-extensions = cythonize(extensions, compiler_directives={'language_level' : '3'})
-
 # since we interface the c stuff with numpy, it's another hard
 # requirement at build-time
 import numpy as np
@@ -72,7 +93,7 @@
     author='Andrew Hoopes',
     author_email='freesurfer@nmr.mgh.harvard.edu',
     url='https://github.com/freesurfer/surfa',
-    python_requires='>=3.6',
+    python_requires='>=3.8',
     packages=packages,
     ext_modules=extensions,
     include_dirs=include_dirs,
@@ -84,4 +105,5 @@
         'Natural Language :: English',
         'Topic :: Scientific/Engineering',
     ],
+    **setup_opts,
 )

tools/audit_wheel.sh

@@ -0,0 +1,9 @@
+#!/bin/bash -eo pipefail
+set -x
+
+PY_MINOR=$(python -c "import sys; print(sys.version_info.minor)")
+if [ "$PY_MINOR" -lt 11 ]; then
+  echo "Not checking abi3audit for Python $PY_MINOR < 3.11"
+  exit 0
+fi
+abi3audit --strict --report --verbose "$1"