tests.yml

name: Tests

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

env:
  FORCE_COLOR: 1

jobs:

  packaging:
    name: Python packaging
    uses: tskit-dev/.github/.github/workflows/python-packaging.yml@v15
    with:
      pyproject-directory: python
      cli-test-cmd: tskit --help

  test-c:
    name: C tests
    uses: tskit-dev/.github/.github/workflows/c-tests.yml@v15
    with:
      library-directory: c
    secrets: inherit

  test-python-c:
    name: Python-C tests
    uses: tskit-dev/.github/.github/workflows/python-c-tests.yml@v15
    with:
      tests: python/tests/test_python_c.py python/tests/test_dict_encoding.py
      pyproject-directory: python
    secrets: inherit


  test:
    name: Python
    uses: tskit-dev/.github/.github/workflows/python-tests.yml@v15
    with:
      os: ${{ matrix.os }}
      python-version: ${{ matrix.python }}
      pyproject-directory: python
      coverage-directory: python/tskit
    secrets: inherit
    strategy:
      matrix:
        python: [ 3.11, 3.13 ]
        os:  [ macos-latest, ubuntu-24.04, windows-latest ]


  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@0.13.0
      with:
        access_token: ${{ github.token }}

    - name: 'Checkout'
      uses: actions/checkout@v6.0.2

    - 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

  bespoke-python-test:
    name: Bespoke Python tests
    runs-on: ubuntu-24.04

    steps:
      - name: Cancel Previous Runs
        uses: styfle/cancel-workflow-action@0.13.0
        with:
          access_token: ${{ github.token }}

      - name: Checkout
        uses: actions/checkout@v6.0.2
        with:
          submodules: true

      - name: Install uv and set the python version
        uses: astral-sh/setup-uv@v6
        with:
          python-version: 3.11
          version: "0.10.0"

      - name: Install Python dependencies
        working-directory: python
        run: uv sync --locked --group test --no-default-groups

      - 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 --locked --group test --no-default-groups \
            python -c "import tskit;tskit.Tree.generate_star(5).tree_sequence.draw_svg(path='test.svg')"

      - name: Run JIT code coverage
        run: |
          NUMBA_DISABLE_JIT=1 uv run --locked --project=python --no-default-groups\
            pytest --cov=python/tskit --cov-report=xml --cov-branch \
            python/tests/test_jit.py

      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v5.5.2
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          fail_ci_if_error: true
          files: coverage.xml
          disable_search: true
          verbose: true
          flags: python-tests-no-jit

      - name: Build example LWT interface code and test
        working-directory: python/lwt_interface/
        run: |
          make allchecks
          uv run --project=../ --group=test pytest -vs

      - name: Build cython example LWT interface code and run
        working-directory: python/lwt_interface/cython_example
        run: make


  bespoke-c-test:
    name: Bespoke C tests
    runs-on: ubuntu-24.04

    steps:
      - name: Cancel Previous Runs
        uses: styfle/cancel-workflow-action@0.13.0
        with:
          access_token: ${{ github.token }}

      - name: Checkout
        uses: actions/checkout@v6.0.2
        with:
          submodules: true

      - name: Install system deps
        run: |
          sudo apt-get update
          sudo apt-get install -y libcunit1-dev ninja-build clang

      - name: Install uv
        uses: astral-sh/setup-uv@v6
        with:
          version: "0.10.0"

      - name: Install uv deps
        run: |
          uv tool install meson==1.10.1

      - name: Configure code
        run: CFLAGS=-D_TSK_BIG_TABLES CPPFLAGS=-D_TSK_BIG_TABLES meson setup build-bt c/

      - name: Compile
        run: ninja -C build-bt

      - name: Run tests
        run: ninja -C build-bt test


      - name: Test building with meson subproject
        run: |
          meson build-subproject c/tests/meson-subproject
          ninja -C build-subproject
          ./build-subproject/example

      - name: Install shared library and hand-compile program.
        run: |
          meson build-install c --prefix=/usr
          sudo ninja -C build-install install
          clang c/examples/api_structure.c -I c/subprojects/kastore -o api_structure -ltskit
          ./api_structure

      - name: Run example make file
        run: |
          make -C c/examples