.travis.yml

language: cpp
dist: jammy

matrix:
  include:
    - name: "linux gcc-11"
      os: linux
      addons:
        apt:
          packages:
            - g++-11
            - parallel
      env:
        - MATRIX_EVAL="CC=gcc-11 && CXX=g++-11 && BUILD_TYPE=Release"
    - name: "linux gcc-12"
      os: linux
      addons:
        apt:
          packages:
            - g++-12
            - parallel
      env:
        - MATRIX_EVAL="CC=gcc-12 && CXX=g++-12 && BUILD_TYPE=Release"

    - name: "linux gcc-11 (coverage)"
      os: linux
      addons:
        apt:
          packages:
            - g++-11
            - parallel
            - lcov
      env:
        - MATRIX_EVAL="CC=gcc-11 && CXX=g++-11 && BUILD_TYPE=Coverage && GCOV=gcov-11"

before_install:
  - eval "${MATRIX_EVAL}"
  - python3 -m pip install --upgrade pip
  - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
  - bash miniconda.sh -b -p $HOME/miniconda
  - source "$HOME/miniconda/etc/profile.d/conda.sh"
  - conda config --set always_yes yes --set changeps1 no
  - conda update -q conda
  - conda info -a
  - conda activate base

install:
  - python3 -m pip install "pandas>=1.2.0"
  - python3 -m pip install "multitax>=1.3.1"
  - python3 -m pip install "parameterized>=0.9.0"
  - if [ "$BUILD_TYPE" == "Coverage" ]; then 
      python3 -m pip install coverage;
    fi
  - conda install -c bioconda -c conda-forge "raptor=3.0.1"
  - mkdir build && cd build 
  - cmake -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DVERBOSE_CONFIG=ON -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -DCONDA=OFF ..
  - cat compile_commands.json
  - cmake --build . -- -j2
  - ctest -VV .
  - sudo make install
  - cd ..

script:
  - ganon-build --version
  - ganon-classify --version
  - raptor --version
  - if [ "$BUILD_TYPE" == "Coverage" ]; then 
      python3 -m coverage run --omit="/usr/*,tests/*" -m unittest discover -s tests/ganon/integration/ -v;
    else
      python3 -m unittest discover -s tests/ganon/integration/ -v &&
      python3 setup.py install --user &&
      ganon -h;
    fi

after_success:
  - if [ "$BUILD_TYPE" == "Coverage" ]; then 
      lcov --gcov-tool $(which ${GCOV}) -d . -c -o coverage_cpp.lcov &&
      python3 -m coverage xml -o coverage_py.xml &&
      curl -Os https://uploader.codecov.io/latest/linux/codecov &&
      chmod +x codecov &&
      ./codecov --nonZero -X search --file coverage_py.xml --file coverage_cpp.lcov;
    fi

notifications:
  email: false