Modernize Build System: Migrate from setup.py to CMake + scikit-build-core (#126)

.github/workflows/python-app.yml

@@ -1,7 +1,7 @@
-# This workflow will install Python dependencies and run tests
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+# This workflow will install Python dependencies, build simuPOP, and run tests
+# across multiple platforms (Linux, macOS, Windows) and Python versions.
 
-name: SimuPOP
+name: simuPOP CI
 
 on:
   push:
@@ -13,30 +13,192 @@ permissions:
   contents: read
 
 jobs:
-  build:
+  build-linux:
     runs-on: ubuntu-latest
-    timeout-minutes: 60
+    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@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
-      # - name: Install boost
-      #   run: |
-      #     sudo apt-get install libboost1.74-all-dev
-      #     ln -s /usr/include/boost/ ./boost_1_74_0
-      - name: Install dependencies
+
+      - 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: Install simuPOP
-        run: python setup.py install
-      - name: Run tests
+
+      - 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