ci.yml

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

name: CI

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

permissions:
  contents: read

jobs:
  test:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
        os: [windows-latest, macOS-latest, ubuntu-latest]
    steps:
    - uses: actions/checkout@v4
      with:
        submodules: "recursive"
    - name: Set up Python
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install oldest-supported-numpy==2023.10.25
        # --ignore-requires-python ensures docs deps don't break install on early python versions
        if [ -f requirements.txt ]; then pip install --ignore-requires-python -r requirements.txt; fi
        pip install -e . 
    - name: Lint with flake8
      run: |
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
    - name: Test with pytest
      run: |
        python -m pytest
  
  coverage:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.11"]
        os: [ubuntu-latest]
    steps:
    - uses: actions/checkout@v4
      with:
        submodules: "recursive"
    - name: Set up Python
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    # - name: Setup LCOV
    #   uses: hrishikesh-kadam/setup-lcov@v1        
    - name: Install dependencies
      run: |
        sudo apt update -yy
        sudo apt install -yy lcov
        python -m pip install --upgrade pip
        pip install wheel
        pip install oldest-supported-numpy==2023.10.25
        # --ignore-requires-python ensures docs deps don't break install on early python versions
        if [ -f requirements.txt ]; then pip install --ignore-requires-python -r requirements.txt; fi
        rm -rf Empirical/.git
    - name: Build phylotrackpy 
      run: |
        make coverage
    - name: Test with pytest
      run: |
        python -m pytest --cov=. --cov-report=lcov
        lcov --output-file coverage.cpp --capture --directory .
        lcov --output-file coverage.cpp --extract coverage.cpp "*"
    - name: Upload coverage reports to Codecov
      uses: codecov/codecov-action@v4
      with:
        files: "coverage.cpp, coverage.lcov, Empirical/include/emp/Evolve/Systematics.hpp"
        token: ${{ secrets.CODECOV_TOKEN }}
        verbose: true      

  build_wheels:
    name: Build wheels on ${{ matrix.os }}
    needs: []
    # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, windows-latest, macos-13, macos-14]

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: "recursive"
      - name: Build wheels
        uses: pypa/cibuildwheel@v2.21.3
      - uses: actions/upload-artifact@v4
        with:
          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
          path: ./wheelhouse/*.whl

  build_sdist:
    name: Build source distribution
    needs: []
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
        with:
          submodules: "recursive"
      - name: Build sdist
        run: pipx run build --sdist

      - uses: actions/upload-artifact@v4
        with:
          name: cibw-sdist
          path: dist/*.tar.gz

  # Regression test borrowed from https://github.com/mmore500/hstrat/blob/ba7b19d0f0561303b6bf789d5024a323aa5993fc/.github/workflows/ci.yaml#L201
  packaging-sdist:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout
        uses: actions/checkout@v4
        with:
          submodules: "recursive"        
      - name: Build sdist
        run: |
          python3 -m venv env
          source env/bin/activate
          python3 -m pip install -r requirements.txt
          python3 setup.py sdist
          tree dist
          deactivate
      - name: Upgrade pip
        run: python3 -m pip install pip --upgrade
      - name: Install from sdist
        run: python3 -m pip install dist/*.tar.gz
      - name: Test install
        run: |
          find . -type f -name '*.py' -exec rm {} \;
          python3 -c "import phylotrackpy; print(phylotrackpy.__version__)"

  upload_pypi:
    needs: [build_wheels, build_sdist, test]
    runs-on: ubuntu-latest
    environment: pypi
    permissions:
      id-token: write
    # upload to PyPI on every tag starting with 'v'
    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
    # alternatively, to publish when a GitHub Release is created, use the following rule:
    # if: github.event_name == 'release' && github.event.action == 'published'
    steps:
      - uses: actions/download-artifact@v4
        with:
          # unpacks default artifact into dist/
          # if `name: artifact` is omitted, the action will create extra parent dir
          pattern: cibw-*
          path: dist
          merge-multiple: true

      - uses: pypa/gh-action-pypi-publish@v1.8.12
        with:
          user: __token__
          password: ${{ secrets.PYPI_API_TOKEN }}

  paper:
    runs-on: ubuntu-latest
    name: Paper Draft
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - name: Build draft PDF
        uses: openjournals/openjournals-draft-action@master
        with:
          journal: joss
          # This should be the path to the paper within your repo.
          paper-path: joss/paper.md
      - name: Upload
        uses: actions/upload-artifact@v4
        with:
          name: paper
          # This is the output path where Pandoc will write the compiled
          # PDF. Note, this should be the same directory as the input
          # paper.md
          path: joss/paper.pdf