tests.yml

name: Tests

on:
  pull_request:
  push:
    branches: [main]

jobs:
  test:
    name: Python
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        python: [3.8, 3.9]
        os: [macos-latest, ubuntu-latest, windows-latest]
        sys: [mingw64, ucrt64]
        env: [x86_64, ucrt-x86_64]
        exclude:
          - os: macos-latest
            sys: ucrt64
          - os: macos-latest
            sys: mingw64
            env: ucrt-x86_64
          - os: ubuntu-latest
            sys: ucrt64
          - os: ubuntu-latest
            sys: mingw64
            env: ucrt-x86_64
          - os: windows-latest
            sys: ucrt64
            env: x86_64
          - os: windows-latest
            sys: mingw64
            env: ucrt-x86_64

    defaults:
      run:
        shell: bash -l {0}
    steps:
      - name: Cancel Previous Runs
        uses: styfle/cancel-workflow-action@0.6.0
        with:
          access_token: ${{ github.token }}

      - name: Checkout
        uses: actions/checkout@v2

      - name: Install Conda
        uses: mamba-org/provision-with-micromamba@main
        with:
          environment-name: anaconda-client-env
          environment-file: requirements/CI-conda/ci-environment.yml
          cache-env: true
          extra-specs: |
            python=${{ matrix.python }}

      - name: Setup MSYS2 ${{matrix.sys}}
        uses: msys2/setup-msys2@v2
        if: matrix.os == 'windows-latest'
        with:
          msystem: ${{matrix.sys}}
          release: false
          install: >-
            git
            base-devel
            msys2-devel
            mingw-w64-${{matrix.env}}-zstd
            mingw-w64-${{matrix.env}}-zlib
            mingw-w64-${{matrix.env}}-toolchain
            mingw-w64-${{matrix.env}}-cmake
            mingw-w64-${{matrix.env}}-autotools

      - name: Cache SLiM build
        if: matrix.os == 'windows-latest'
        id: cache-slim
        uses: actions/cache@v3.0.5 # latest version is broken https://github.com/actions/cache/issues/891, so pinning to 3.0.5
        with:
          path: D:\a\pyslim\pyslim\SLiM
          key: ${{runner.os}}-${{matrix.sys}}-${{matrix.env}}-key

      - name: Build SLiM windows
        if: ( matrix.os == 'windows-latest'  && steps.cache-slim.outputs.cache-hit != 'true' )
        shell: msys2 {0}
        run: |
          git clone https://github.com/messerlab/SLiM.git
          mkdir -p SLiM/Release
          cd SLiM/windows_compat/gnulib
          touch --date="`date`" aclocal.m4 Makefile.am configure configure.ac config.h.in Makefile.in
          cd ../..
          cd Release
          cmake -G"MSYS Makefiles" -DCMAKE_BUILD_TYPE=Release ..
          make -j 2

      - name: Install SLiM macos / linux
        if: (matrix.os == 'macos-latest' || matrix.os == 'ubuntu-latest')
        run: |
          micromamba install slim -y

      - name: Run tests
        shell: bash -l {0}
        run: |
          micromamba info
          micromamba list
          export PATH=$PWD/SLiM/Release:$PATH 
          which slim
          slim -v
          python -m pytest \
            -n 0 \
            -v \
            --cov=pyslim \
            --cov-branch \
            --cov-report=term-missing \
            --cov-report=xml \
            tests


      - name: upload coverage report to codecov
        uses: codecov/codecov-action@v3
        with:
          fail_ci_if_error: true
          env_vars: OS,PYTHON
          token: ${{ secrets.CODECOV_TOKEN }}