tests.yml

name: Tests

on:
  pull_request:
  merge_group:
  push:
    branches: [main, test]

jobs:
  pre-commit:
    name: Lint
    uses: tskit-dev/.github/.github/workflows/lint.yml@v2

  test:
    name: Python
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        python: [ "3.10", 3.13 ]
        os:  [ macos-latest, ubuntu-24.04, windows-latest ]
    defaults:
      run:
        shell: bash
    steps:
      - name: Cancel Previous Runs
        uses: styfle/cancel-workflow-action@0.12.1
        with:
          access_token: ${{ github.token }}

      - name: Checkout
        uses: actions/checkout@v4.2.2

      - name: Install OSX libs
        if: matrix.os == 'macos-latest'
        run: |
          brew install libxml2 libxslt

      - name: Fix windows symlinks
        working-directory: python
        if: matrix.os == 'windows-latest'
        run: |
          rm -r lib
          mkdir lib
          cp -r --dereference ../c/subprojects lib/.
          cp -r --dereference ../c/tskit lib/.
          cp ../c/tskit.h lib/.

      - name: Install uv and set the python version
        uses: astral-sh/setup-uv@v6
        with:
          python-version: ${{ matrix.python }}
          version: "0.8.15"
      
      - name: Install dependencies
        working-directory: python
        run: |
          uv venv
          uv pip install -r pyproject.toml --extra test
          # Remove tskit installed as a dep of msprime
          uv pip uninstall tskit

      - name: Build module
        working-directory: python
        run: |
          uv run --no-sync python setup.py build_ext --inplace

      - name: Minidom test
        working-directory: python
        # Importing either IPython or pytest causes import of xml.dom.minidom
        # So to actually test that tskit imports it, we need a minimal test
        run: |
          uv run --no-sync python -c "import tskit;tskit.Tree.generate_star(5).tree_sequence.draw_svg(path='test.svg')"

      - name: Run JIT code coverage
        working-directory: python
        run: |
          NUMBA_DISABLE_JIT=1 uv run --no-sync python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 tests/test_jit.py

      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v5.4.0
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          working-directory: python
          fail_ci_if_error: false
          flags: python-tests-no-jit
          name: codecov-umbrella
          verbose: true
      - name: Run tests
        working-directory: python
        run: |
          if [[ "${{ matrix.os }}" == "windows-latest" ]]; then
            uv run --no-sync python -m pytest -x --skip-slow --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests
          else
            uv run --no-sync python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests
          fi

      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v5.4.0
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          working-directory: python
          fail_ci_if_error: false
          flags: python-tests
          name: codecov-umbrella
          verbose: true


  test-numpy1:
    name: Numpy 1.x
    runs-on: ubuntu-24.04
    defaults:
      run:
        shell: bash
    steps:
      - name: Cancel Previous Runs
        uses: styfle/cancel-workflow-action@0.12.1
        with:
          access_token: ${{ github.token }}

      - name: Checkout
        uses: actions/checkout@v4.2.2

      - name: Setup Python
        uses: actions/setup-python@v5.4.0
        with:
          python-version: '3.12'

      - name: Install uv
        uses: astral-sh/setup-uv@v6
        with:
          version: "0.8.15"

      - name: Install dependencies
        working-directory: python
        run: |
          uv venv
          uv pip install -r pyproject.toml --extra test
          uv pip uninstall tskit
          uv pip install "numpy<2"

      - name: Build module
        working-directory: python
        run: |
          uv run --no-sync python setup.py build_ext --inplace

      - name: Run tests with numpy 1.x
        working-directory: python
        run: |
          uv run --no-sync python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 tests/test_lowlevel.py tests/test_highlevel.py

      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v5.4.0
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          working-directory: python
          fail_ci_if_error: false
          flags: python-tests-numpy1
          name: codecov-numpy1
          verbose: true

  msys2:
    runs-on: windows-latest
    strategy:
      matrix:
        include:
        - { sys: mingw32, env: i686 }
        - { sys: mingw64, env: x86_64 }
    name: Windows (${{ matrix.sys }}, ${{ matrix.env }})
    defaults:
      run:
        shell: msys2 {0}
    steps:
    - name: Cancel Previous Runs
      uses: styfle/cancel-workflow-action@0.12.1
      with:
        access_token: ${{ github.token }}

    - name: 'Checkout'
      uses: actions/checkout@v4.2.2

    - name: Setup MSYS2 ${{matrix.sys}}
      uses: msys2/setup-msys2@v2.27.0
      with:
        msystem: ${{matrix.sys}}
        update: true
        install: >-
          git
          mingw-w64-${{matrix.env}}-toolchain
          mingw-w64-${{matrix.env}}-ninja
          mingw-w64-${{matrix.env}}-meson
          mingw-w64-${{matrix.env}}-cunit

    - name: Build
      working-directory: c
      run: |
        meson build -Dbuild_examples=false
        ninja -C build

    - name: Run tests
      working-directory: c
      run: |
        ninja -C build test