.travis.yml

# https://travis-ci.org/ParBLiSS/kmerind

language: cpp

sudo: false

#compiler:
#    - gcc
#    - clang

#different compilers
#env:
#    - envCXX=g++-4.8 envCC=gcc-4.8
#    - envCXX=g++-4.9 envCC=gcc-4.9
#    - envCXX=g++-5 envCC=gcc-5
#    - envCXX=clang++-3.5 envCC=clang-3.5
#    - envCXX=clang++-3.6 envCC=clang-3.6
#    - envCXX=clang++-3.7 envCC=clang-3.7

#addons:
#  apt:
#    sources:
#      - ubuntu-toolchain-r-test
#    packages:
#      - openmpi
#    - llvm-toolchain-precise-3.5
#    - llvm-toolchain-precise-3.6
#    - llvm-toolchain-precise-3.7


# include specific compiler combinations combinations
matrix:
    include:
      - compiler: gcc
        addons:
          apt:
            sources:
              - ubuntu-toolchain-r-test
            packages:
              - openmpi-bin
              - libopenmpi-dev
              - gcc-4.8
              - g++-4.8
        env: envCXX=g++-4.8 envCC=gcc-4.8
      - compiler: gcc
        addons:
          apt:
            sources:
              - ubuntu-toolchain-r-test
            packages:
              - openmpi-bin
              - libopenmpi-dev
              - gcc-4.9
              - g++-4.9
        env: envCXX=g++-4.9 envCC=gcc-4.9
      - compiler: gcc
        addons:
          apt:
            sources:
              - ubuntu-toolchain-r-test
            packages:
              - openmpi-bin
              - libopenmpi-dev
              - gcc-5
              - g++-5
        env: envCXX=g++-5 envCC=gcc-5
      - compiler: clang
        addons:
          apt:
            sources:
              - ubuntu-toolchain-r-test
              - llvm-toolchain-precise-3.5
            packages:
              - openmpi-bin
              - libopenmpi-dev
              - clang-3.5
        env: envCXX=clang++-3.5 envCC=clang-3.5
      - compiler: clang
        addons:
          apt:
            sources:
              - ubuntu-toolchain-r-test
              - llvm-toolchain-precise-3.6
            packages:
              - openmpi-bin
              - libopenmpi-dev
              - clang-3.6
        env: envCXX=clang++-3.6 envCC=clang-3.6
      - compiler: clang
        addons:
          apt:
            sources:
              - ubuntu-toolchain-r-test
              - llvm-toolchain-precise-3.7
            packages:
              - openmpi-bin
              - libopenmpi-dev
              - clang-3.7
        env: envCXX=clang++-3.7 envCC=clang-3.7
      - compiler: clang
        addons:
          apt:
            sources:
              - ubuntu-toolchain-r-test
              - llvm-toolchain-precise-3.8
            packages:
              - openmpi-bin
              - libopenmpi-dev
              - clang-3.8
        env: envCXX=clang++-3.8 envCC=clang-3.8
      

before_install:
    - pip install --user codecov

#addons:
#  apt:
#    sources:
#    - ubuntu-toolchain-r-test
#    - llvm-toolchain-precise-3.5
#    - llvm-toolchain-precise-3.6
#    - llvm-toolchain-precise-3.7
#    packages:
#    - gcc-4.8
#    - g++-4.8
#    - gcc-4.9
#    - g++-4.9
#    - gcc-5
#    - g++-5
#    - clang-3.5
#    - clang-3.6
#    - clang-3.7

# caching of the whole `local` directory. Can't cache only the one for this
# `env`, because otherwise the different instances will overwrite the cache.
# For the first test-run, the build has to be run sequentially (limit parallel
# workers to 1) so that the cache can be correctly initialized. Once the cache
# is build, parallel workers can be re-enabled.
#cache:
#  directories:
#    - $HOME/local

before_script:
    # check if gcc or clang
    - if [ "$CXX" = "clang++" ]; then export COMPILER="clang"; else export COMPILER="gnu"; fi
#    # install MPI - only 1 configuration for each compiler does this
    - export MPI=openmpi
    # set compiler to newer versions
    - export CXX="$envCXX" CC="$envCC" OMPI_CC="$envCC" OMPI_CXX="$envCXX"
    # set up MPI location
    - export PATH=$PATH:$HOME/local/$MPI/bin
    - export LIBRARY_PATH=$LIBRARY_PATH:$HOME/local/$MPI/lib
    - export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/local/$MPI/lib
    # print out version information
    - $CXX --version
    - mpiexec --version
    - export SRC_DIR=`pwd`
    # compile sparsehash
    - cd ext/sparsehash
    - ./configure CXXFLAGS=-std=c++11
    - make
    - cd $SRC_DIR
    # prepare build kmerind
    - mkdir build
    - cd build
    # first pass cmake
    - if [ "$COMPILER" = "clang" ]; then cmake -DCMAKE_BUILD_TYPE=Release -DENABLE_TESTING=ON -DLOG_ENGINE=PRINTF -DUSE_MPI=ON -DUSE_OPENMP=OFF -DUSE_SIMD_IF_AVAILABLE=ON -DENABLE_BENCHMARKING=OFF ../;
        else cmake -DCMAKE_BUILD_TYPE=Release -DENABLE_TESTING=ON -DLOG_ENGINE=PRINTF -DUSE_MPI=ON -DUSE_OPENMP=ON -DUSE_SIMD_IF_AVAILABLE=ON -DENABLE_BENCHMARKING=OFF ../; fi
    # do it again else the gtests will not be built
    - if [ "$COMPILER" = "clang" ]; then cmake -DBUILD_TEST_APPLICATIONS=ON -DENABLE_COVERAGE=OFF ../;
        else cmake -DBUILD_TEST_APPLICATIONS=ON -DENABLE_COVERAGE=ON ../; fi
    # build kmerind.  here so that if build fails, the tests are not run.
    - make

script:
    # run tests.
    - make test 
    - ./bin/testFASTA_load
    - mpiexec -np 4 ./bin/testFASTA_load
    - ./bin/testFASTQ_load
    - mpiexec -np 4 ./bin/testFASTQ_load
    - ./bin/testKmerIndex-fasta
    - mpiexec -np 4 ./bin/testKmerIndex-fasta
    - ./bin/testKmerIndex-fastq
    - mpiexec -np 4 ./bin/testKmerIndex-fastq
    - ./bin/test_de_bruijn_graph_construction
    - mpiexec -np 4 ./bin/test_de_bruijn_graph_construction

after_success:
  # only collect coverage if compiled with gcc
  #- if [ "$CXX" = "g++-4.8" ]; then codecov --comp ${SRC_DIR}/config/comp.txt --gcov-exec gcov-4.8; fi
  #- if [ "$CXX" = "g++-4.9" ]; then codecov --comp ${SRC_DIR}/config/comp.txt --gcov-exec gcov-4.9; fi
  - if [ "$CXX" = "g++-5" ]; then codecov --gcov-exec gcov-5; fi