python-app.yml

# This workflow will install Python dependencies, build simuPOP, and run tests
# across multiple platforms (Linux, macOS, Windows) and Python versions.

name: simuPOP CI

on:
  push:
    branches: [ "master" ]
  pull_request:
    branches: [ "master" ]

permissions:
  contents: read

jobs:
  build-linux:
    runs-on: ubuntu-latest
    timeout-minutes: 90
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.9", "3.10", "3.11", "3.12"]

    steps:
      - uses: actions/checkout@v4

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          cache: 'pip'

      - name: Install system dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y swig zlib1g-dev cmake ninja-build

      - name: Install Python dependencies
        run: |
          python -m pip install --upgrade pip
          pip install build scikit-build-core cmake ninja
          pip install -r requirements.txt

      - name: Build and install simuPOP
        run: pip install -v .

      - name: Run tests (short allele type)
        run: python ./test/run_tests.py short -j2

      - name: Run tests (binary allele type)
        run: python ./test/run_tests.py binary -j2

  build-macos-intel:
    runs-on: macos-13
    timeout-minutes: 90
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.10", "3.11", "3.12"]

    steps:
      - uses: actions/checkout@v4

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          cache: 'pip'

      - name: Install system dependencies
        run: |
          brew install swig libomp cmake ninja

      - name: Install Python dependencies
        run: |
          python -m pip install --upgrade pip
          pip install build scikit-build-core cmake ninja
          pip install -r requirements.txt

      - name: Build and install simuPOP
        env:
          OpenMP_ROOT: /usr/local/opt/libomp
        run: pip install -v .

      - name: Run tests (short allele type)
        run: python ./test/run_tests.py short -j2

      - name: Run tests (binary allele type)
        run: python ./test/run_tests.py binary -j2

  build-macos-arm:
    runs-on: macos-14
    timeout-minutes: 90
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.10", "3.11", "3.12"]

    steps:
      - uses: actions/checkout@v4

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          cache: 'pip'

      - name: Install system dependencies
        run: |
          brew install swig libomp cmake ninja

      - name: Install Python dependencies
        run: |
          python -m pip install --upgrade pip
          pip install build scikit-build-core cmake ninja
          pip install -r requirements.txt

      - name: Build and install simuPOP
        env:
          OpenMP_ROOT: /opt/homebrew/opt/libomp
        run: pip install -v .

      - name: Run tests (short allele type)
        run: python ./test/run_tests.py short -j2

      - name: Run tests (binary allele type)
        run: python ./test/run_tests.py binary -j2

  build-windows:
    runs-on: windows-latest
    timeout-minutes: 120
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.10", "3.11", "3.12"]

    steps:
      - uses: actions/checkout@v4

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          cache: 'pip'

      - name: Install SWIG
        run: choco install swig -y

      - name: Install zlib via vcpkg (static)
        run: |
          vcpkg install zlib:x64-windows-static

      - name: Install Python dependencies
        run: |
          python -m pip install --upgrade pip
          pip install build scikit-build-core cmake ninja
          pip install -r requirements.txt

      - name: Build and install simuPOP
        run: |
          $toolchain = "$env:VCPKG_INSTALLATION_ROOT\scripts\buildsystems\vcpkg.cmake"
          pip install -v . --config-settings=cmake.args="-DCMAKE_TOOLCHAIN_FILE=$toolchain;-DVCPKG_TARGET_TRIPLET=x64-windows-static"

      - name: Run tests (short allele type)
        run: python ./test/run_tests.py short -j2

      - name: Run tests (binary allele type)
        run: python ./test/run_tests.py binary -j2

  # Full test suite on Linux (all allele types)
  full-tests-linux:
    runs-on: ubuntu-latest
    timeout-minutes: 180
    needs: build-linux
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.11"]

    steps:
      - uses: actions/checkout@v4

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          cache: 'pip'

      - name: Install system dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y swig zlib1g-dev cmake ninja-build

      - name: Install Python dependencies
        run: |
          python -m pip install --upgrade pip
          pip install build scikit-build-core cmake ninja
          pip install -r requirements.txt

      - name: Build and install simuPOP
        run: pip install -v .

      - name: Run all tests
        run: python ./test/run_tests.py