tests.yml

name: tests
on:
  # Run tests on every push to the main branch,
  # on every pull request, and once a week (every monday at 05:00)
  push:
  pull_request:
  schedule:
    - cron: "0 5 * * 1"
jobs:
  canceller:
    runs-on: ubuntu-latest
    steps:
      - name: Cancel previous runs
        uses: styfle/cancel-workflow-action@0.12.1
  coverage:
    if: github.event_name != 'schedule' || (github.event_name == 'schedule' && github.repository == 'messerlab/slim')
    runs-on: ubuntu-24.04
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4
      - name: Set up GCC
        run: |
          sudo apt-get install gcc-12 g++-12 && \
          sudo update-alternatives \
            --install /usr/bin/gcc gcc /usr/bin/gcc-12 100 \
            --slave /usr/bin/g++ g++ /usr/bin/g++-12
      - name: Build with coverage
        run: |
          mkdir Coverage && cd Coverage && \
          cmake -DCMAKE_BUILD_TYPE=Debug -DCOVERAGE=ON .. && \
          make -j 2 && \
          env CTEST_OUTPUT_ON_FAILURE=1 make test
      - name: Generate coverage report
        run: |
          sudo apt-get update && \
          sudo apt-get install -y lcov && \
          lcov --gcov-tool gcov-12 --ignore-errors gcov,mismatch --rc geninfo_unexecuted_blocks=1 --capture --directory Coverage --output-file coverage.info && \
          lcov --gcov-tool gcov-12 --ignore-errors gcov,mismatch,unused --remove coverage.info '/usr/*' '*/gsl/*' '*/eidos_zlib/*' --output-file coverage.info
      - name: Upload coverage reports to Codecov
        uses: codecov/codecov-action@v5
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          files: coverage.info
          fail_ci_if_error: true
  tests-Unix-CLI:
    if: github.event_name != 'schedule' || (github.event_name == 'schedule' && github.repository == 'messerlab/slim')
    strategy:
      fail-fast: false
      matrix:
        include:
          # Ubuntu with the oldest supported GCC
          # BCH 2/12/2025: Ubuntu 22.04 is being discontinued, shifting forward
          - { os: ubuntu-22.04, gcc: 9, python: 3.9 }
          - { os: ubuntu-24.04, gcc: 12, python: 3.12 }
          # macOS, oldest supported version
          # (macos-10.15, macos-11, macos-12, and macos-13 were removed by GitHub)
          - { os: macos-14, python: 3.9 }
          # macOS, newest supported version
          - { os: macos-26, python: 3.13 }

    runs-on: ${{ matrix.os }}
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4
      - name: Setup Miniforge
        uses: conda-incubator/setup-miniconda@v3
        with:
          miniforge-version: latest
          activate-environment: anaconda-client-env
          python-version: ${{ matrix.python }}
      - name: Get Date
        id: get-date
        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
        shell: bash
      - name: Cache Conda env
        uses: actions/cache@v3
        with:
          path: ${{ env.CONDA }}/envs
          key:
            conda-${{ runner.os }}--python-${{ matrix.python }}--${{ runner.arch }}--${{
            steps.get-date.outputs.today }}-${{
            hashFiles('treerec/tests/environment.yml') }}-${{ env.CACHE_NUMBER}}
        env:
          # Increase this value to reset cache if
          # treerec/tests/environment.yml has not changed
          CACHE_NUMBER: 0
        id: cache
      - name: Update environment
        run: conda env update -n anaconda-client-env -f treerec/tests/environment.yml
        if: steps.cache.outputs.cache-hit != 'true'
      - name: Workaround for gcc-11
        if: startsWith(matrix.os, 'ubuntu') && matrix.gcc == 11
        run: |
          sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y && \
          sudo apt-get update -y
      - name: Set up default GCC (in Ubuntu)
        if: startsWith(matrix.os, 'ubuntu')
        run: |
          sudo apt-get install gcc-${{ matrix.gcc }} g++-${{ matrix.gcc }} && \
          sudo update-alternatives \
            --install /usr/bin/gcc gcc /usr/bin/gcc-${{ matrix.gcc }} 100 \
            --slave /usr/bin/g++ g++ /usr/bin/g++-${{ matrix.gcc }}
      - name: Build and test (Debug)
        run: |
          mkdir Debug && \
          cd Debug && \
          cmake -DCMAKE_BUILD_TYPE=Debug .. && \
          make -j 2 && \
          # Show any output from the test program whenever the test fails
          env CTEST_OUTPUT_ON_FAILURE=1 make test
      - name: Build and test (Release)
        run: |
          mkdir Release && \
          cd Release && \
          cmake -DCMAKE_BUILD_TYPE=Release .. && \
          make -j 2 && \
          # Show any output from the test program whenever the test fails
          env CTEST_OUTPUT_ON_FAILURE=1 make test
      - name: Treesequence tests
        shell: bash -el {0}
        run: |
          conda activate anaconda-client-env && \
          export PATH=$PATH:$PWD/Release && \
          echo $PATH && \
          cd treerec/tests && python -m pytest -xv
          
  tests-Windows-CLI:
    if: github.event_name != 'schedule' || (github.event_name == 'schedule' && github.repository == 'messerlab/slim')
    runs-on: windows-latest
    strategy:
      fail-fast: false
      matrix:
        include:
          - { sys: mingw64, env: x86_64, python: 3.9 }
          - { sys: ucrt64, env: ucrt-x86_64, python: 3.9 }
    defaults:
      run:
        shell: msys2 {0}
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4
      - name: Setup MSYS2 ${{matrix.sys}}
        uses: msys2/setup-msys2@v2
        with:
          msystem: ${{matrix.sys}}
          update: true
          install: >-
            git
            base-devel
            msys2-devel
            mingw-w64-${{matrix.env}}-toolchain
            mingw-w64-${{matrix.env}}-cmake
      - name: Setup Miniforge
        uses: conda-incubator/setup-miniconda@v3
        with:
          miniforge-version: latest
          activate-environment: anaconda-client-env
          auto-update-conda: true
          python-version: ${{ matrix.python }}
      - name: Get Date
        id: get-date
        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
        shell: bash
      - name: Cache Conda env
        uses: actions/cache@v3
        env:
          # Increase this value to reset cache if treerec/tests/environment.yml has not changed
          CACHE_NUMBER: 0
        with:
          # Use faster GNU tar
          enableCrossOsArchive: true
          path: D:\conda_pkgs_dir
          key:
            conda-${{ runner.os }}--python-${{ matrix.python }}--${{ runner.arch }}--${{
            steps.get-date.outputs.today }}-${{
            hashFiles('treerec/tests/environment.yml') }}-${{ env.CACHE_NUMBER}}
        id: cache
      - uses: conda-incubator/setup-miniconda@v3
        with:
          activate-environment: anaconda-client-env
          environment-file: treerec/tests/environment.yml
          pkgs-dirs: D:\conda_pkgs_dir
      - name: Update environment
        shell: bash -el {0}
        run: conda env update -n anaconda-client-env -f treerec/tests/environment.yml
        if: steps.cache.outputs.cache-hit != 'true'
      - name: Build and test (Debug)
        run: |
          cd windows_compat/gnulib && \
          touch --date="`date`" aclocal.m4 Makefile.am configure configure.ac config.h.in Makefile.in && \
          cd ../.. && \
          mkdir Debug && \
          cd Debug && \
          cmake -G"MSYS Makefiles" -DCMAKE_BUILD_TYPE=Debug .. && \
          make -j 2 && \
          # Show any output from the test program whenever the test fails
          env CTEST_OUTPUT_ON_FAILURE=1 make test
      - name: Build and test (Release)
        run: |
          cd windows_compat/gnulib && \
          touch --date="`date`" aclocal.m4 Makefile.am configure configure.ac config.h.in Makefile.in && \
          cd ../.. && \
          mkdir Release && \
          cd Release && \
          cmake -G"MSYS Makefiles" -DCMAKE_BUILD_TYPE=Release .. && \
          make -j 2 && \
          # Show any output from the test program whenever the test fails
          env CTEST_OUTPUT_ON_FAILURE=1 make test
      - name: Treesequence tests
        shell: bash -el {0}
        run: |
          conda activate anaconda-client-env && \
          export PATH=$PATH:$PWD/Release && \
          echo $PATH && \
          cd treerec/tests && python -m pytest -xv

  tests-Unix-GUI:
    if: github.event_name != 'schedule' || (github.event_name == 'schedule' && github.repository == 'messerlab/slim')
    strategy:
      fail-fast: false
      matrix:
        include:
          # BCH 2/12/2025: Ubuntu 22.04 is being discontinued, shifting forward
          # Ubuntu 22.04 with the oldest supported Qt5 and GCC.
          - { os: ubuntu-22.04, qt: 5.9.5, gcc: 9 }
          # Ubuntu 22.04 with last official LTS Qt5 and GCC.
          - { os: ubuntu-22.04, qt: 5.15.2, gcc: 12 }
          # Ubuntu 24.04 with the most recent Qt6 and GCC.
          - { os: ubuntu-22.04, qt: 6.8.2, gcc: 12 }
          # macos-12 and macos-13 were removed by GitHub,
          # so we can't CI with Qt 5.X on macOS any more, oh well
          # old macOS with last official LTS Qt5
          #- { os: macos-13, qt: 5.15.2 }
          # old macOS ARM64 with older Qt6
          - { os: macos-14, qt: 6.7.3 }
          # macOS Intel with older Qt6
          - { os: macos-15-intel, qt: 6.7.3 }
          # new macOS with a very recent Qt6
          - { os: macos-26, qt: 6.9.2 }
    runs-on: ${{ matrix.os }}
    env:
      CXXFLAGS: -D NO_QT_VERSION_ERROR
    defaults:
      run:
        shell: bash
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4
      - name: Workaround for gcc-11
        if: startsWith(matrix.os, 'ubuntu') && matrix.gcc == 11
        run: |
          sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y && \
          sudo apt-get update -y
      - name: Set up default GCC (in Ubuntu)
        if: startsWith(matrix.os, 'ubuntu')
        run: |
          sudo apt-get install gcc-${{ matrix.gcc }} g++-${{ matrix.gcc }} && \
          sudo update-alternatives \
            --install /usr/bin/gcc gcc /usr/bin/gcc-${{ matrix.gcc }} 100 \
            --slave /usr/bin/g++ g++ /usr/bin/g++-${{ matrix.gcc }}

      - name: Install Qt
        uses: jurplel/install-qt-action@v4
        with:
          version: ${{ matrix.qt }}
      - name: Release build with SLiMGUI
        run: |
          mkdir Release && \
          cd Release  && \
          cmake -D BUILD_SLIMGUI=ON -DCMAKE_BUILD_TYPE=Release ..  && \
          make -j 2 && \
          # Show any output from the test program whenever the test fails
          env CTEST_OUTPUT_ON_FAILURE=1 make test

  tests-Windows-GUI:
    if: github.event_name != 'schedule' || (github.event_name == 'schedule' && github.repository == 'messerlab/slim')
    strategy:
      fail-fast: false
      matrix:
        include:
          - { sys: mingw64, env: x86_64 }
          - { sys: ucrt64, env: ucrt-x86_64 }
    runs-on: windows-latest
    defaults:
      run:
        shell: msys2 {0}
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4
      - name: Setup MSYS2 ${{matrix.sys}}
        uses: msys2/setup-msys2@v2
        with:
          msystem: ${{matrix.sys}}
          update: true
          install: >-
            git
            base-devel
            msys2-devel
            mingw-w64-${{matrix.env}}-toolchain
            mingw-w64-${{matrix.env}}-cmake
            mingw-w64-${{matrix.env}}-qt5-base
      - name: Release build
        run: |
          cd . && \
          cd windows_compat/gnulib && \
          touch --date="`date`" aclocal.m4 Makefile.am configure configure.ac config.h.in Makefile.in && \
          cd ../.. && \
          mkdir Release && \
          cd Release && \
          cmake -G"MSYS Makefiles" -DBUILD_SLIMGUI=ON -DCMAKE_BUILD_TYPE=Release .. && \
          make -j 2 && \
          # Show any output from the test program whenever the test fails
          env CTEST_OUTPUT_ON_FAILURE=1 make test
  tests-windows-latest-pacman:
    if: github.event_name != 'schedule' || (github.event_name == 'schedule' && github.repository == 'messerlab/slim')
    runs-on: windows-latest
    strategy:
      fail-fast: false
      matrix:
        include:
          - { sys: mingw64, env: x86_64 }
          - { sys: ucrt64, env: ucrt-x86_64 }
    defaults:
      run:
        shell: msys2 {0}
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4
      - name: Setup MSYS2 ${{matrix.sys}}
        uses: msys2/setup-msys2@v2
        with:
          msystem: ${{matrix.sys}}
          update: true
          install: >-
            mingw-w64-${{matrix.env}}-slim-simulator
      - name: Test
        run: |
          eidos -testEidos
          slim -testEidos
          slim -testSLiM