ENH: abi3

.coveragerc

@@ -0,0 +1,13 @@
+[run]
+branch = True
+source = sleepecg
+omit =
+    */examples/*
+    */setup.py
+
+[report]
+exclude_lines =
+    pragma: no cover
+    if __name__ == .__main__.:
+    @abstractmethod
+    @abstractclassmethod

.github/workflows/cibuildwheel.yml

@@ -0,0 +1,153 @@
+name: Test
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+
+on:
+  pull_request:
+    paths-ignore:
+    - 'docs/**'
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+jobs:
+  style:
+    name: Check style
+    runs-on: ubuntu-22.04
+    timeout-minutes: 2
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+    - uses: pre-commit/action@v3.0.1
+
+  build_wheels:
+    needs: style
+    strategy:
+      matrix:
+        os: [ubuntu-22.04, windows-2022, macos-15, macos-13]
+        arch: [native]
+        include:
+          - os: ubuntu-22.04
+            arch: aarch64
+      fail-fast: false
+    timeout-minutes: 15  # Linux ~1 min, Windows ~4 min, aarch64 emulated ~8 min with tests (~3 min without)
+    name: cibuildwheel (${{ matrix.os }} ${{ matrix.arch }})
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set wheel tests to be skipped on emulated archs on PRs
+        run: |
+          if [[ "${{ github.event_name }}" == "pull_request" ]] && [[ "${{ matrix.arch }}" == "aarch64" ]]; then
+            echo "CIBW_TEST_SKIP=*" | tee -a $GITHUB_ENV
+          fi
+        shell: bash
+      # For aarch64 support https://cibuildwheel.pypa.io/en/stable/faq/#emulation
+      - uses: docker/setup-qemu-action@v3
+        with:
+          platforms: all
+        if: runner.os == 'Linux' && matrix.arch == 'aarch64'
+      - name: Build wheels and run tests
+        uses: pypa/cibuildwheel@v2.22.0
+        env:
+          CIBW_ARCHS: ${{ matrix.arch }}
+      - uses: actions/upload-artifact@v4
+        with:
+          name: artifact-${{ matrix.os }}-${{ matrix.arch }}
+          path: ./wheelhouse/*.whl
+
+  test:
+    needs: build_wheels
+    strategy:
+      matrix:
+        os: [ubuntu-22.04, windows-2022, macos-15, macos-13]
+        python-version: ['3.12']
+        include:
+          - os: ubuntu-22.04
+            python-version: '3.13'
+      fail-fast: false
+    name: Test wheels (${{ matrix.os }} py${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 5
+    defaults:
+      run:
+        shell: bash -eo pipefail {0}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: artifact-${{ matrix.os }}-native
+          merge-multiple: true
+          path: dist
+      - run: ls -al dist
+      - name: Triage dependencies
+        run: |
+          if [[ "${{ matrix.python-version }}" != "3.13" ]]; then
+            echo "PIP_EXTRA=wfdb numpy<2 numba pytest-error-for-skips" | tee -a $GITHUB_ENV
+            echo "PYTEST_EXTRA=--error-for-skips" | tee -a $GITHUB_ENV
+          fi
+      - run: python -m pip install ./dist/*.whl pytest pytest-cov edfio $PIP_EXTRA --only-binary="numpy,numba,edfio"
+      - run: pytest -rfEXs --cov=sleepecg --cov-report=xml --tb=short --cov-branch --color=yes $PYTEST_EXTRA tests/
+      - uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+        if: success() || failure()
+
+  build_sdist:
+    needs: style
+    name: Build source distribution
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        name: Install Python
+        with:
+          python-version: 3.12
+      - name: Build sdist
+        run: |
+          set -eo pipefail
+          python -m pip install build numpy
+          python -m build --sdist
+      - uses: actions/upload-artifact@v4
+        with:
+          name: artifact-sdist
+          path: dist/*.tar.gz
+
+  check_wheels:
+    needs: [build_wheels, build_sdist]
+    name: Check wheels and source distribution
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: artifact-*
+          merge-multiple: true
+          path: dist
+      - run: ls -al dist
+        shell: bash
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+      - run: python -m pip install twine
+      - run: python -m twine check --strict dist/*
+
+  upload-pypi:
+    name: Upload to PyPI
+    needs: [check_wheels, test]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release'
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: artifact-*
+          merge-multiple: true
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@v1.12.3

.gitignore

@@ -6,3 +6,6 @@
 __pycache__/
 site/
 sleepecg.egg-info/
+/build
+/coverage.xml
+/.coverage

codecov.yml

@@ -0,0 +1,25 @@
+comment: false
+github_checks:  # too noisy, even though "a" interactively disables them
+  annotations: false
+
+codecov:
+  notify:
+    require_ci_to_pass: false
+
+coverage:
+  status:
+    patch:
+      default:
+        informational: true
+        target: 95%
+        if_no_uploads: error
+        if_not_found: success
+        if_ci_failed: failure
+    project:
+      default: false
+      library:
+        informational: true
+        target: 90%
+        if_no_uploads: error
+        if_not_found: success
+        if_ci_failed: failure

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools", "setuptools-scm", "numpy"]
+requires = ["setuptools", "setuptools-scm", "wheel", "numpy>=2,<3"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -11,7 +11,7 @@ authors = [
     {name = "Clemens Brunner", email = "clemens.brunner@gmail.com"},
 ]
 readme = "README.md"
-requires-python = ">= 3.9, < 3.13"
+requires-python = ">= 3.9"
 classifiers = [
     "License :: OSI Approved :: BSD License",
     "Operating System :: Microsoft :: Windows",
@@ -27,7 +27,7 @@ classifiers = [
 ]
 keywords = ["sleep", "ecg", "qrs", "peak"]
 dependencies = [
-    "numpy >= 1.25.0, < 2.0.0",
+    "numpy >= 1.25.0, < 3.0.0",
     "PyYAML >= 5.4.0",
     "requests >= 2.25.0",
     "scipy >= 1.7.0",
@@ -64,6 +64,8 @@ cibw = [  # cibuildwheel uses this for running the test suite
     "edfio >= 0.4.0",
     "numba >= 0.59.1",
     "wfdb >= 3.4.0",
+    # https://github.com/MIT-LCP/wfdb-python/pull/511
+    "numpy < 2.0.0",  # TODO: just for wfdb!
 ]
 
 [project.urls]
@@ -77,6 +79,14 @@ test-requires = "pytest"
 test-extras = "cibw"
 test-command = "pytest {package}"
 skip = 'pp* *musllinux*'
+build = "cp39-*"  # abi3
+
+[[tool.cibuildwheel.overrides]]
+select = "*"
+inherit.repair-wheel-command = "append"
+repair-wheel-command = [
+  "pipx run abi3audit --strict --report {wheel}",
+]
 
 [tool.cibuildwheel.linux]
 manylinux-x86_64-image = "manylinux2014"
@@ -87,6 +97,10 @@ archs = "x86_64 arm64"
 
 [tool.cibuildwheel.windows]
 archs = "AMD64"
+before-build = "pip install delvewheel"
+repair-wheel-command = [
+  "delvewheel repair -w {dest_dir} {wheel}",
+]
 
 [tool.mypy]
 ignore_missing_imports = true

setup.py

@@ -1,12 +1,34 @@
 import numpy as np
 from setuptools import Extension, setup
+from wheel.bdist_wheel import bdist_wheel
+
+# Following https://github.com/joerick/python-abi3-package-sample
+
+
+# Currently set to 3.9. If this is bumped for example to 3.10, the hex
+# in the Extension needs to change to 0x030A0000, and the cibuildwheel `build`
+# selector needs to change in pyproject.toml
+
+class bdist_wheel_abi3(bdist_wheel):
+    def get_tag(self) -> tuple:
+        python, abi, plat = super().get_tag()
+
+        if python.startswith("cp"):
+            # on CPython, our wheels are abi3 and compatible back to 3.6
+            return "cp39", "abi3", plat
+
+        return python, abi, plat
+
 
 setup(
     ext_modules=[
         Extension(
             "sleepecg._heartbeat_detection",
             ["src/sleepecg/_heartbeat_detection.c"],
             include_dirs=[np.get_include()],
+            define_macros=[("Py_LIMITED_API", "0x03090000")],
+            py_limited_api=True,
         ),
     ],
+    cmdclass={"bdist_wheel": bdist_wheel_abi3},
 )