tests.yml

name: Tests

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

jobs:
  pre-commit:
    name: Lint
    runs-on: ubuntu-latest
    steps:
      - name: Cancel Previous Runs
        uses: styfle/cancel-workflow-action@0.12.1
        with:
          access_token: ${{ github.token }}
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: '3.10'
      - name: install clang-format
        if: steps.clang_format.outputs.cache-hit != 'true'
        run: |
          python -m venv env
          source env/bin/activate
          pip install clang-format==6.0.1
      - uses: pre-commit/action@v3.0.0

  benchmark:
    name: Benchmark
    runs-on: ubuntu-latest
    steps:
      - name: Cancel Previous Runs
        uses: styfle/cancel-workflow-action@0.12.1
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: '3.11'
          cache: 'pip'
          cache-dependency-path: python/requirements/benchmark.txt
      - name: Install deps
        run: pip install -r python/requirements/benchmark.txt
      - name: Build module
        run: |
          cd python
          python setup.py build_ext --inplace
      - name: Run benchmarks
        run: |
          cd python/benchmark
          pip uninstall -y tskit
          python run.py
      - name: Upload Results
        uses: actions/upload-artifact@v4
        with:
          name: benchmark-results
          path: python/benchmark

  test:
    name: Python
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        python: [ 3.9, 3.12 ]
        os:  [ macos-latest, ubuntu-latest, 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@v3

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

      - name: Cache conda and dependencies
        id: cache
        uses: actions/cache@v4
        with:
          path: ${{ env.CONDA }}/envs
          key: ${{ runner.os }}-${{ runner.arch }}-${{ matrix.python}}-conda-v1-${{ hashFiles('python/requirements/CI-tests-conda/requirements.txt') }}-${{ hashFiles('python/requirements/CI-tests-pip/requirements.txt') }}

      - name: Install Conda
        uses: conda-incubator/setup-miniconda@v3
        if: steps.cache.outputs.cache-hit != 'true'
        with:
          activate-environment: anaconda-client-env
          python-version: ${{ matrix.python }}
          channels: conda-forge
          channel-priority: strict
          auto-update-conda: true

      - 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: Fix windows .profile
        if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest'
        run: |
          cp ~/.bash_profile ~/.profile

      - name: Install conda deps
        if: steps.cache.outputs.cache-hit != 'true'
        shell: bash -l {0} #We need a login shell to get conda
        run: |
          conda install --yes --file=python/requirements/CI-tests-conda/requirements.txt

      - name: Install pip deps
        if: steps.cache.outputs.cache-hit != 'true'
        shell: bash -l {0}
        run: |
          pip install -r python/requirements/CI-tests-pip/requirements.txt
          # Remove tskit installed by conda
          pip uninstall -y tskit

      - name: Build module
        working-directory: python
        run: |
          source ~/.profile
          conda activate anaconda-client-env
          python setup.py build_ext --inplace

      - name: Run tests
        working-directory: python
        run: |
          source ~/.profile
          conda activate anaconda-client-env
          python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests

      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v4
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          working-directory: python
          fail_ci_if_error: false
          flags: python-tests
          name: codecov-umbrella
          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

    - name: Setup MSYS2 ${{matrix.sys}}
      uses: msys2/setup-msys2@v2
      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