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Modernize Build System: Migrate from setup.py to CMake + scikit-build-core (#126) #31

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

Modernize Build System: Migrate from setup.py to CMake + scikit-build-core (#126) #31

Workflow file for this run

.github/workflows/python-app.yml at 95b5d24
# 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:
runs-on: macos-latest
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:
# Help CMake find libomp on macOS
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 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
# 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