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ENH: abi3 (cbrnr#251)
* ENH: abi3 * FIX: More * FIX: Ref * FIX: Wheel tag * FIX: Ig * FIX: Move on * FIX: Ver * FIX: Non seq * FIX: Naming * FIX: Append * FIX: Verbose * MAINT: Only test emulated on main * FIX: More * FIX: maybe * FIX: Name * FIX: More * FIX: Fixes * FIX: Cleaner * FIX: Missed * FIX: More * FIX: Add * FIX: Name * FIX: Cov
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‎.coveragerc

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

‎.github/workflows/cibuildwheel.yml

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

‎.github/workflows/release.yml

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‎.github/workflows/test.yml

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‎.gitignore

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__pycache__/
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site/
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sleepecg.egg-info/
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/build
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/coverage.xml
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/.coverage

‎codecov.yml

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

‎pyproject.toml

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

‎setup.py

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

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