Parameterize CTMCOnTree by the alignment type. #1417
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| name: Build and test | |
| on: | |
| push: | |
| branches: | |
| - "*" | |
| pull_request: | |
| branches: | |
| - "*" | |
| jobs: | |
| build: | |
| strategy: | |
| matrix: | |
| name: [ubuntu-gcc-10, | |
| # ubuntu-gcc-11-sanitize, | |
| ubuntu-gcc-11-debugoptimized, | |
| ubuntu-gcc-11-DEBUG_MACHINE, | |
| ubuntu-gcc-11, | |
| ubuntu-gcc-12, | |
| ubuntu-clang-13, | |
| macos-xcode-14, | |
| windows | |
| ] | |
| include: | |
| - name: ubuntu-gcc-10 | |
| os: ubuntu-20.04 | |
| compiler: gcc | |
| version: "10" | |
| buildtype: "release" | |
| arch: "linux64" | |
| # - name: ubuntu-gcc-11-sanitize | |
| # os: ubuntu-22.04 | |
| # compiler: gcc | |
| # version: "11" | |
| # buildtype: "release" | |
| # sanitize: "address" | |
| # arch: "linux64" | |
| - name: ubuntu-gcc-11-debugoptimized | |
| os: ubuntu-22.04 | |
| compiler: gcc | |
| version: "11" | |
| buildtype: "debugoptimized" | |
| arch: "linux64" | |
| - name: ubuntu-gcc-11-DEBUG_MACHINE | |
| os: ubuntu-22.04 | |
| compiler: gcc | |
| version: "11" | |
| buildtype: "debugoptimized" | |
| cxxflags: "-DDEBUG_MACHINE=1" | |
| arch: "linux64" | |
| - name: ubuntu-gcc-11 | |
| os: ubuntu-22.04 | |
| compiler: gcc | |
| version: "11" | |
| buildtype: "release" | |
| arch: "linux64" | |
| - name: ubuntu-gcc-12 | |
| os: ubuntu-22.04 | |
| compiler: gcc | |
| version: "12" | |
| buildtype: "release" | |
| arch: "linux64" | |
| - name: ubuntu-clang-13 | |
| os: ubuntu-22.04 | |
| compiler: clang | |
| version: "13" | |
| buildtype: "release" | |
| arch: "linux64" | |
| - name: macos-xcode-14 | |
| os: macos-12 | |
| compiler: xcode | |
| version: "14" | |
| buildtype: "release" | |
| arch: "mac64" | |
| - name: windows | |
| os: ubuntu-22.04 | |
| compiler: mingw | |
| version: "N/A" | |
| buildtype: "release" | |
| arch: "win64" | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| - name: Install (Linux) | |
| if: runner.os == 'Linux' && matrix.name != 'windows' | |
| run: | | |
| sudo apt-get install -y pandoc ccache | |
| sudo rm -rf /usr/local/share/boost | |
| sudo apt-get install -y libboost-all-dev nlohmann-json3-dev librange-v3-dev libeigen3-dev libcairo2-dev | |
| if [ "${{ matrix.compiler }}" = "gcc" ]; then | |
| # For newer GCCs, maybe. | |
| # sudo add-apt-repository ppa:ubuntu-toolchain-r/ppa | |
| # sudo apt-get update | |
| sudo apt-get install -y g++-${{ matrix.version }} | |
| echo "CC=ccache gcc-${{ matrix.version }}" >> $GITHUB_ENV | |
| echo "CXX=ccache g++-${{ matrix.version }}" >> $GITHUB_ENV | |
| else | |
| sudo apt-get install -y clang-${{ matrix.version }} | |
| echo "CC=ccache clang-${{ matrix.version }}" >> $GITHUB_ENV | |
| echo "CXX=ccache clang++-${{ matrix.version }}" >> $GITHUB_ENV | |
| fi | |
| - name: Install (Linux -> Windows [cross]) | |
| if: matrix.name == 'windows' | |
| run: | | |
| # For mingw/gcc-12. | |
| cat /etc/apt/sources.list | |
| sudo sed -i 's/jammy/lunar/g' /etc/apt/sources.list | |
| sudo apt-get update | |
| sudo apt-get install -y pandoc ccache | |
| sudo apt-get install -y dos2unix g++-mingw-w64 wine64 zstd | |
| - name: Select XCode version (macOS) | |
| if: runner.os == 'macOS' | |
| uses: maxim-lobanov/setup-xcode@v1 | |
| with: | |
| xcode-version: ${{ matrix.version }} | |
| - name: Install (macOS) | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install pkg-config pandoc ccache coreutils | |
| brew install boost eigen range-v3 nlohmann-json cairo | |
| echo "CC=ccache clang" >> $GITHUB_ENV | |
| echo "CXX=ccache clang++" >> $GITHUB_ENV | |
| - name: Install meson | |
| run: | | |
| python3 -mpip install meson ninja | |
| # Caches for different branches are isolated, so we don't need to put the branch name into the key. | |
| # The total size for all caches in a repository is 5Gb. | |
| - name: Prepare ccache timestamp | |
| id: ccache_cache_timestamp | |
| run: | | |
| ccache --set-config=cache_dir=$HOME/.ccache | |
| if [ "${{ runner.os }}" = "Linux" ]; then | |
| stamp=$(date '+%s') | |
| else | |
| stamp=$(gdate '+%s') | |
| fi | |
| echo "${stamp}" | |
| echo "timestamp=${stamp}" >> $GITHUB_OUTPUT | |
| - name: ccache cache files | |
| # uses: actions/cache@v2 | |
| uses: pat-s/[email protected] | |
| with: | |
| path: ~/.ccache | |
| key: ${{ matrix.name }}-ccache-${{ steps.ccache_cache_timestamp.outputs.timestamp }} | |
| restore-keys: | | |
| ${{ matrix.name }}-ccache- | |
| - name: Make windows sysroot and generate cross file | |
| if: matrix.name == 'windows' | |
| # This command also generates the cross file | |
| run: | | |
| ${GITHUB_WORKSPACE}/scripts/make_winroot.sh | |
| - name: Configure | |
| run: | | |
| if [ "${{ runner.os }}" = "macOS" ]; then | |
| export CFLAGS="-mmacosx-version-min=10.15" | |
| export CXXFLAGS="-mmacosx-version-min=10.15" | |
| export LDFLAGS="-mmacosx-version-min=10.15" | |
| fi | |
| CPPARGS="-g" | |
| if [ "${{ matrix.cxxflags }}" != "" ] ; then | |
| CPPARGS="$CPPARGS ${{ matrix.cxxflags }}" | |
| fi | |
| if [ "${{ matrix.arch }}" = "win64" ]; then | |
| ARGS="${ARGS} --cross-file=win64-cross.txt" | |
| fi | |
| if [ "${{ runner.os }}" = "Linux" ] && [ "${{ matrix.name }}" != "windows" ] && [ "${{ matrix.sanitize }}" != "" ] ; then | |
| # Address sanitizer can't find its dylibs on OS X? | |
| ARGS="${ARGS} -Db_sanitize=${{ matrix.sanitize }}" | |
| fi | |
| echo meson setup build --prefix=$HOME/local --buildtype=${{ matrix.buildtype }} -Dcpp_args="$CPPARGS" ${ARGS} | |
| meson setup build --prefix=$HOME/local --buildtype=${{ matrix.buildtype }} -Dcpp_args="$CPPARGS" ${ARGS} | |
| - name: Upload meson log if configure failed | |
| uses: actions/upload-artifact@v3 | |
| if: failure() | |
| with: | |
| name: meson-log-${{ matrix.name }} | |
| path: '/home/runner/work/BAli-Phy/BAli-Phy/build/meson-logs/meson-log.txt' | |
| - name: Build | |
| run: | | |
| ccache -p | |
| ccache -s | |
| ninja -C build install -j4 | |
| ccache -s | |
| - name: Get version | |
| id: get_version | |
| run: | | |
| echo "version=$(echo $GITHUB_REF | cut -d / -f 3)" >> $GITHUB_OUTPUT | |
| - name: Copy shared libs (Linux) | |
| if: matrix.arch == 'linux64' | |
| run: | | |
| OUTPUT=$HOME/local | |
| cp $(${CXX} -print-file-name=libstdc++.so.6) $OUTPUT/lib/bali-phy/libstdc++.so.6 | |
| for libname in $(ldd ${OUTPUT}/bin/bali-phy | grep libboost | sed s'/\s*lib\(boost.*\) =>.*/\1/') ; do | |
| echo cp $($CXX --print-file-name lib${libname}) ${OUTPUT}/lib/bali-phy/ | |
| cp $($CXX --print-file-name lib${libname}) ${OUTPUT}/lib/bali-phy/ | |
| done | |
| ldd ${OUTPUT}/bin/bali-phy | |
| - name: Copy shared libs (Windows) | |
| if: matrix.arch == 'win64' | |
| run: | | |
| OUTPUT=$HOME/local | |
| CXX=x86_64-w64-mingw32-g++-posix | |
| # Copy compiler DLLS | |
| for libname in gcc_s_seh-1 stdc++-6 ssp-0 winpthread-1 ; do | |
| cp $($CXX --print-file-name lib${libname}.dll) ${OUTPUT}/bin | |
| done | |
| cp /home/runner/win_root/mingw64/bin/libboost_*.dll ${OUTPUT}/bin | |
| - name: Test | |
| run: | | |
| export seed=$RANDOM | |
| if [ "${{ matrix.name }}" = "windows" ] ; then | |
| export WINEPATH=$(winepath -w $HOME/local/bin) | |
| BALIPHY="wine bali-phy" | |
| else | |
| export PATH=$HOME/local/bin:$PATH | |
| BALIPHY=bali-phy | |
| fi | |
| echo "Running tests with seed=$seed" | |
| echo ::group::Basic tests | |
| ${BALIPHY} help | |
| cp $HOME/local/share/doc/bali-phy/examples/5S-rRNA/5d-muscle.fasta . | |
| ${BALIPHY} --seed=$seed 5d-muscle.fasta --test | |
| ${BALIPHY} --seed=$seed 5d-muscle.fasta --iter=20 | |
| # Skip the rest of the tests if this is a DEBUG_MACHINE test. | |
| debugmachine=false | |
| case "${{ matrix.name }}" in | |
| *-DEBUG_MACHINE) debugmachine=true ;; | |
| esac | |
| if [ "$debugmachine" = "false" ] ; then | |
| echo ::group::Test suite | |
| cd tests | |
| ./run-tests.py ${BALIPHY} --seed=$seed | |
| cd | |
| echo ::endgroup:: | |
| fi | |
| git clone https://gitlab.com/testiphy/testiphy.git | |
| cd testiphy | |
| git checkout no-root-knuckle | |
| rm -rf tests/likelihood/one-sequence | |
| echo ::group::testiphy variable A | |
| ./testiphy ${BALIPHY} --seed=$seed --fix=alignment --fix=tree | |
| echo ::endgroup:: | |
| echo ::group::testiphy fixed A | |
| ./testiphy ${BALIPHY} --seed=$seed -Inone --fix=alignment --fix=tree | |
| echo ::endgroup:: | |
| - name: Upload tests if they failed | |
| uses: actions/upload-artifact@v3 | |
| if: failure() | |
| with: | |
| name: tests-${{ matrix.name }} | |
| path: tests | |