Merge branch 'cbrnr:main' into accelerometer_feature_addition

.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 +1,151 @@
+name: Test
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+
+on:
+  pull_request:
+    paths-ignore:
+    - 'docs/**'
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+jobs:
+  style:
+    name: Check style
+    runs-on: ubuntu-22.04
+    timeout-minutes: 2
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+    - uses: pre-commit/[email protected]
+
+  build_wheels:
+    needs: style
+    strategy:
+      matrix:
+        os: [ubuntu-22.04, windows-2022, macos-15, macos-13]
+        arch: [native]
+        include:
+          - os: ubuntu-22.04
+            arch: aarch64
+      fail-fast: false
+    timeout-minutes: 15  # Linux ~1 min, Windows ~4 min, aarch64 emulated ~8 min with tests (~3 min without)
+    name: cibuildwheel (${{ 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/[email protected]
+        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: |
+          echo "PIP_EXTRA=wfdb numba pytest-error-for-skips" | tee -a $GITHUB_ENV
+          echo "PYTEST_EXTRA=--error-for-skips" | tee -a $GITHUB_ENV
+      - 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/[email protected]

.gitignore

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

.pre-commit-config.yaml

@@ -1,17 +1,17 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.5
+    rev: v0.9.2
     hooks:
       - id: ruff
         args: [ --fix ]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.14.1
     hooks:
     - id: mypy
       exclude: ^tests|^examples
-      args: [--python-version=3.9]
+      args: [--python-version=3.10]
       additional_dependencies:
       - types-PyYAML
       - types-requests

CHANGELOG.md

@@ -1,10 +1,14 @@
 ## [UNRELEASED] - YYYY-MM-DD
 ### Added
 - Add support to store NSRR token in environment variable or user config ([#243](https://github.com/cbrnr/sleepecg/pull/243) by [Simon Pusterhofer](https://github.com/simon-p-2000))
+- Add Python 3.13+ support by transforming wheel builds using ABI3 mode ([#251](https://github.com/cbrnr/sleepecg/pull/251) by [Eric Larson](https://github.com/larsoner))
 
 ### Changed
 - Split `get_config` function into `get_config` and `get_config_value` to get the entire configuration (as a dictionary) or an individual configuration key, respectively ([#229](https://github.com/cbrnr/sleepecg/pull/225) by [Clemens Brunner](https://github.com/cbrnr))
 
+### Removed
+- Remove Python 3.9 support ([#241](https://github.com/cbrnr/sleepecg/pull/241) by [Clemens Brunner](https://github.com/cbrnr))
+
 ### Fixed
 - Fix `plot_ecg` for newer versions of Matplotlib ([#225](https://github.com/cbrnr/sleepecg/pull/225) by [Clemens Brunner](https://github.com/cbrnr))
 

README.md

@@ -1,4 +1,4 @@
-![Python](https://img.shields.io/pypi/pyversions/sleepecg.svg?logo=python&logoColor=white)
+![Python](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2Fcbrnr%2Fsleepecg%2Frefs%2Fheads%2Fmain%2Fpyproject.toml&logo=python&logoColor=white)
 [![PyPI](https://img.shields.io/pypi/v/sleepecg)](https://pypi.org/project/sleepecg/)
 [![Docs](https://readthedocs.org/projects/sleepecg/badge/?version=latest)](https://sleepecg.readthedocs.io/en/stable/index.html)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.05411/status.svg)](https://doi.org/10.21105/joss.05411)

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