shift to a vector of chromosomes, of length 1 #1248
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| 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-20.04 | |
| steps: | |
| - name: Cancel previous runs | |
| uses: styfle/[email protected] | |
| tests-Unix-CLI: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # Ubuntu with the oldest supported GCC | |
| # (used to be 4.8, but with 20.04 it is 7, sadly). | |
| - {os: ubuntu-20.04, gcc: 7, python: 3.8} | |
| - {os: ubuntu-20.04, gcc: 11, python: 3.9} | |
| # macOS, oldest supported version | |
| # (macos-10.15 and macos-11 were removed by GitHub) | |
| - {os: macos-12, python: 3.8} | |
| # macOS, newest supported version (haven't tried macos-14 yet) | |
| - {os: macos-13, python: 3.9} | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| - name: Setup Mambaforge | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| activate-environment: anaconda-client-env | |
| use-mamba: 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 | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: | |
| conda-${{ runner.os }}--python-${{ matrix.python }}--${{ runner.arch }}--${{ | |
| steps.get-date.outputs.today }}-${{ | |
| hashFiles('treerec/tests/environment.yml') }}-${{ env.CACHE_NUMBER}} | |
| env: | |
| # Increase this value to reset cache if | |
| # treerec/tests/environment.yml has not changed | |
| CACHE_NUMBER: 0 | |
| id: cache | |
| - name: Update environment | |
| run: | |
| mamba env update -n anaconda-client-env -f treerec/tests/environment.yml | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| - name: Workaround for gcc-11 | |
| if: startsWith(matrix.os, 'ubuntu') && matrix.gcc == 11 | |
| run: | | |
| sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y && \ | |
| sudo apt-get update -y | |
| - name: Set up default GCC (in Ubuntu) | |
| if: startsWith(matrix.os, 'ubuntu') | |
| run: | | |
| sudo apt-get install gcc-${{ 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++-${{ matrix.gcc }} | |
| - name: Build and test (Debug) | |
| run: | | |
| mkdir Debug && \ | |
| cd Debug && \ | |
| cmake -D CMAKE_BUILD_TYPE=Debug .. && \ | |
| make -j 2 && make test | |
| - name: Build and test (Release) | |
| run: | | |
| mkdir Release && \ | |
| cd Release && \ | |
| cmake -D CMAKE_BUILD_TYPE=Release .. && \ | |
| make -j 2 && make test | |
| - name: Treesequence tests | |
| shell: bash -el {0} | |
| run: | | |
| conda activate anaconda-client-env && \ | |
| export PATH=$PATH:$PWD/Release && \ | |
| echo $PATH && \ | |
| cd treerec/tests && python -m pytest -xv | |
| tests-Windows-CLI: | |
| runs-on: windows-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - {sys: mingw64, env: x86_64, python: 3.8} | |
| - {sys: ucrt64, env: ucrt-x86_64, python: 3.8} | |
| 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 Mambaforge | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| activate-environment: anaconda-client-env | |
| use-mamba: true | |
| 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 | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: | |
| conda-${{ runner.os }}--python-${{ matrix.python }}--${{ runner.arch }}--${{ | |
| steps.get-date.outputs.today }}-${{ | |
| hashFiles('treerec/tests/environment.yml') }}-${{ env.CACHE_NUMBER}} | |
| env: | |
| # Increase this value to reset cache if | |
| # treerec/tests/environment.yml has not changed | |
| CACHE_NUMBER: 0 | |
| id: cache | |
| - name: Update environment | |
| shell: bash -el {0} | |
| run: | |
| mamba env update -n anaconda-client-env -f treerec/tests/environment.yml | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| - name: Build and test (Debug) | |
| run: | | |
| cd windows_compat/gnulib && \ | |
| touch --date="`date`" aclocal.m4 Makefile.am configure configure.ac config.h.in Makefile.in && \ | |
| cd ../.. && \ | |
| mkdir Debug && \ | |
| cd Debug && \ | |
| cmake -G"MSYS Makefiles" -DCMAKE_BUILD_TYPE=Debug .. && \ | |
| make -j 2 && make test | |
| - name: Build and test (Release) | |
| run: | | |
| cd windows_compat/gnulib && \ | |
| touch --date="`date`" aclocal.m4 Makefile.am configure configure.ac config.h.in Makefile.in && \ | |
| cd ../.. && \ | |
| mkdir Release && \ | |
| cd Release && \ | |
| cmake -G"MSYS Makefiles" -DCMAKE_BUILD_TYPE=Release .. && \ | |
| make -j 2 && make test | |
| - name: Treesequence tests | |
| shell: bash -el {0} | |
| run: | | |
| conda activate anaconda-client-env && \ | |
| export PATH=$PATH:$PWD/Release && \ | |
| echo $PATH && \ | |
| cd treerec/tests && python -m pytest -xv | |
| tests-Unix-GUI: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # Ubuntu 20.04 with the oldest supported Qt5 and GCC. | |
| - {os: ubuntu-20.04, qt: 5.9.5, gcc: 7} | |
| # Ubuntu 20.04 with the most recent Qt5 and GCC. | |
| - {os: ubuntu-20.04, qt: 5.15.2, gcc: 11} | |
| # Ubuntu 22.04 with the most recent Qt5 and GCC. | |
| - {os: ubuntu-22.04, qt: 5.15.2, gcc: 12} | |
| # Ubuntu 22.04 with the most recent Qt6 and GCC; this is the min for Qt6 | |
| - {os: ubuntu-22.04, qt: 6.7.2, gcc: 12} | |
| # old macOS with oldest supported Qt5 | |
| - {os: macos-12, qt: 5.9.5} | |
| # new macOS with most recent Qt5 | |
| - {os: macos-13, qt: 5.15.2} | |
| # new macOS with most recent Qt6 | |
| - {os: macos-13, qt: 6.7.2} | |
| 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 -D CMAKE_BUILD_TYPE=Release .. && \ | |
| make -j 2 && make test | |
| tests-Windows-GUI: | |
| 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 && make test | |
| tests-windows-latest-pacman: | |
| 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 |