.travis.yml

language: cpp

#sudo: false # required

matrix:
  include:
    - os: linux
      compiler: gcc
      addons:
        apt:
          sources:
            - ubuntu-toolchain-r-test
          packages:
            - gcc-7
            - g++-7
            - zlib1g-dev # for RocksDB
      env:
        - MATRIX_EVAL="ENV=Linux+gcc-7 && CC=gcc-7 && CXX=g++-7"
      
    - os: linux
      compiler: clang
      addons:
        apt:
          sources:
            - llvm-toolchain-trusty-6.0
            - ubuntu-toolchain-r-test
          packages:
            - clang-6.0
            - zlib1g-dev # for RocksDB
      env:
        - MATRIX_EVAL="ENV=Linux+LLVM_clang-6.0 && CC=clang-6.0 && CXX=clang++-6.0"
      
    - os: osx
      osx_image: xcode9.2 # OS X 10.12 Sierra
      compiler: clang
      env:
        - MATRIX_EVAL="ENV=Osx+clang-9.0-APPL"
        #- MATRIX_EVAL="CC=clang-9.0 && CXX=clang++-9.0" # this screws the Miniconda installation
      
    # this is probably no different from osx+clang. MAC GCC seems to be just an interface to clang.
    - os: osx
      osx_image: xcode9.2 # OS X 10.12 Sierra
      compiler: gcc
      env:
        - MATRIX_EVAL="ENV=Osx+gcc-APPL && CC=gcc && CXX=g++ && gcc --version" # default gcc installed with OSX
        #- MATRIX_EVAL="ENV=Osx+gcc-7 && brew install gcc && brew link --overwrite gcc && CC=gcc-7 && CXX=g++-7" # need to fix conflicts with pre-installed gcc
        
# does nothing
#  exclude:
#    - os : linux
#      compiler: clang
      
#    - os : osx
#      compiler: gcc


before_install:
  - eval "${MATRIX_EVAL}"
  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then wget http://repo.continuum.io/miniconda/Miniconda3-3.7.3-Linux-x86_64.sh -O miniconda.sh ; fi
  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then wget http://repo.continuum.io/miniconda/Miniconda3-3.7.3-MacOSX-x86_64.sh -O miniconda.sh ; fi
  - chmod +x miniconda.sh
  - ./miniconda.sh -b -p $HOME/miniconda
  - export PATH="$HOME/miniconda/bin:$PATH"
  - conda update --yes conda
  - conda config --add channels https://conda.anaconda.org/biobuilds
  # C++14
#  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$CC" == "gcc" ]]; then sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test ; fi
#  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$CC" == "gcc" ]]; then sudo apt-get update -qq ; fi
  
install:
  - conda create --yes -n env_name python=3.5 numpy scipy
  - source activate env_name
  - pip install scikit-bio==0.2.3
  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update ; fi
  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install zlib rocksdb rapidjson ; fi  # brew install gcc5  cmake is installed by default
    # C++14
#  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$CC" == "gcc" ]]; then sudo apt-get install gcc-7 g++-7 ; fi # -qq g++-7
#  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$CC" == "gcc" ]]; then sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-7 60 --slave /usr/bin/g++ g++ /usr/bin/g++-7 ; fi # '90' priority
  # for building RocksDB
#  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install -y zlib1g-dev ; fi # libgflags-dev libsnappy-dev libbz2-dev libzstd-dev  cmake installed by default
  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then pushd ./3rdparty; git clone https://github.com/facebook/rocksdb.git ; popd; fi
  
script:
  - echo "${TRAVIS_BUILD_DIR}" # /home/travis/build/biocore/sortmerna
  # build RocksDB
  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then mkdir -p 3rdparty/rocksdb/build/Release; pushd 3rdparty/rocksdb/build/Release ; fi
  - if [[ "$ENV" == "Linux+gcc-7" ]]; then cmake -E env CXXFLAGS="-Wno-error=maybe-uninitialized" cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Release -DPORTABLE=1 -DWITH_ZLIB=1 -DWITH_TESTS=0 -DWITH_TOOLS=0 -DEXTRA_CXX_FLAGS_RELEASE="-pthread" ../.. ; fi
  - if [[ "$ENV" == "Linux+LLVM_clang-6.0" ]]; then cmake -E env CXXFLAGS="-Wno-error=unused-private-field" cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Release -DPORTABLE=1 -DWITH_ZLIB=1 -DWITH_TESTS=0 -DWITH_TOOLS=0 ../.. ; fi
  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then make; popd ; fi
  # build SortmeRNA
  - mkdir -p build/Release; pushd build/Release
  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Release -DSRC_RAPIDJSON=1 -DSET_ROCKSDB=1 -DEXTRA_CXX_FLAGS_RELEASE="-pthread" -DROCKSDB_INCLUDE_DIR=${TRAVIS_BUILD_DIR}/3rdparty/rocksdb/include -DROCKSDB_LIB_RELEASE=${TRAVIS_BUILD_DIR}/3rdparty/rocksdb/build/Release ../.. ; fi
  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Release -DEXTRA_CXX_FLAGS_RELEASE="-pthread" ../.. ; fi
  - make; popd
  # run tests
  - export PATH="$PWD/build/Release/src/indexdb:$PWD/build/Release/src/sortmerna:$PATH"
  - if [[ "$ENV" == "Linux+gcc-7" ]]; then python ./tests/test_sortmerna.py; fi
  #- if [[ "$ENV" == "Linux+gcc-7" ]]; then python ./tests/test_sortmerna_zlib.py; fi

## END .travis.yml