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Merge pull request #127 from BoPeng/collection
Modernize Build System: Migrate from setup.py to CMake + scikit-build-core (#126)
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‎.github/workflows/python-app.yml‎

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# This workflow will install Python dependencies and run tests
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# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
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# This workflow will install Python dependencies, build simuPOP, and run tests
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# across multiple platforms (Linux, macOS, Windows) and Python versions.
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name: SimuPOP
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name: simuPOP CI
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on:
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push:
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contents: read
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jobs:
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build:
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build-linux:
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runs-on: ubuntu-latest
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timeout-minutes: 60
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timeout-minutes: 90
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.9", "3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@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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cache: 'pip'
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# - name: Install boost
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# run: |
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# sudo apt-get install libboost1.74-all-dev
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# ln -s /usr/include/boost/ ./boost_1_74_0
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- name: Install dependencies
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- name: Install system dependencies
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run: |
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sudo apt-get update
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sudo apt-get install -y swig zlib1g-dev cmake ninja-build
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- name: Install Python dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build scikit-build-core cmake ninja
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pip install -r requirements.txt
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- name: Install simuPOP
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run: python setup.py install
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- name: Run tests
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- name: Build and install simuPOP
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run: pip install -v .
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- name: Run tests (short allele type)
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run: python ./test/run_tests.py short -j2
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- name: Run tests (binary allele type)
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run: python ./test/run_tests.py binary -j2
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build-macos-intel:
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runs-on: macos-13
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timeout-minutes: 90
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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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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cache: 'pip'
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- name: Install system dependencies
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run: |
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brew install swig libomp cmake ninja
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- name: Install Python dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build scikit-build-core cmake ninja
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pip install -r requirements.txt
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- name: Build and install simuPOP
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env:
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OpenMP_ROOT: /usr/local/opt/libomp
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run: pip install -v .
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- name: Run tests (short allele type)
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run: python ./test/run_tests.py short -j2
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- name: Run tests (binary allele type)
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run: python ./test/run_tests.py binary -j2
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build-macos-arm:
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runs-on: macos-14
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timeout-minutes: 90
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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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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cache: 'pip'
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- name: Install system dependencies
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run: |
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brew install swig libomp cmake ninja
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- name: Install Python dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build scikit-build-core cmake ninja
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pip install -r requirements.txt
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- name: Build and install simuPOP
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env:
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OpenMP_ROOT: /opt/homebrew/opt/libomp
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run: pip install -v .
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- name: Run tests (short allele type)
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run: python ./test/run_tests.py short -j2
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- name: Run tests (binary allele type)
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run: python ./test/run_tests.py binary -j2
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build-windows:
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runs-on: windows-latest
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timeout-minutes: 120
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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cache: 'pip'
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- name: Install SWIG
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run: choco install swig -y
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- name: Install zlib via vcpkg (static)
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run: |
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vcpkg install zlib:x64-windows-static
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- name: Install Python dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build scikit-build-core cmake ninja
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pip install -r requirements.txt
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- name: Build and install simuPOP
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run: |
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$toolchain = "$env:VCPKG_INSTALLATION_ROOT\scripts\buildsystems\vcpkg.cmake"
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pip install -v . --config-settings=cmake.args="-DCMAKE_TOOLCHAIN_FILE=$toolchain;-DVCPKG_TARGET_TRIPLET=x64-windows-static"
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- name: Run tests (short allele type)
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run: python ./test/run_tests.py short -j2
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- name: Run tests (binary allele type)
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run: python ./test/run_tests.py binary -j2
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# Full test suite on Linux (all allele types)
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full-tests-linux:
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runs-on: ubuntu-latest
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timeout-minutes: 180
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needs: build-linux
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.11"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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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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cache: 'pip'
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- name: Install system dependencies
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run: |
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sudo apt-get update
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sudo apt-get install -y swig zlib1g-dev cmake ninja-build
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- name: Install Python dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build scikit-build-core cmake ninja
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pip install -r requirements.txt
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- name: Build and install simuPOP
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run: pip install -v .
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- name: Run all tests
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run: python ./test/run_tests.py

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