.travis.yml

#==============================================================================
# FILE: .travis.yml
# Travis CI build configuration
#==============================================================================

# 20190708
#   Build matrix is a Total Mess! Exclude seems to have no action at all. All the
#   logic of 'include' and 'exclude' is unpredictable.
#
#   OSX 'xcode10.2' packages Apple Clang 9.0 based on LLVM 7.0 and doesn't support
#   <filesystem> at ALL (not even experimental)
#
#   LLVM Clang 8.0 screws RocksDB on deprecations and doesn't support <filesystem>
#
#   Wait until LLVM 9.0 which should be ready by the end of this year with 
#   <filesystem> support
#
#   For now only build on Linux with GCC

#os:
#  - linux
#  - osx

#language: cpp
#compiler:
#  - clang
#  - gcc

#dist: xenial
#osx_image: xcode10.2

#addons:
#  apt:
#    sources:
#      - ubuntu-toolchain-r-test
#      - llvm-toolchain-xenial-7
#    packages:
#      - gcc-9
#      - g++-9
#      - clang-7

#sudo: false # required
env:
  global:
    - OAUTH=""
    - DO_DEPLOY=0

matrix:
  include:
    - os: linux
      compiler: gcc
      dist: xenial
      addons:
        apt:
          sources:
            - ubuntu-toolchain-r-test
          packages:
            - gcc-9
            - g++-9
      env:
        - MATRIX_EVAL="ENV=Linux_gcc-9 && CC=gcc-9 && CXX=g++-9"
        - STATIC_LINK=1
        - TEST=0
        - OS_SFX="U16"
      deploy:
        provider: releases
        api_key: "${OAUTH}"
        file: 
          - ${TRAVIS_BUILD_DIR}/dist/sortmerna-${TRAVIS_TAG:1}-Linux-${OS_SFX}-static.sh
          - ${TRAVIS_BUILD_DIR}/dist/sortmerna-${TRAVIS_TAG:1}-Linux-${OS_SFX}-static.deb
        overwrite: true
        skip_cleanup: true
        on:
          tags: true
          condition: $DO_DEPLOY = 1 && $STATIC_LINK = 1
      
#    - os: linux
#      compiler: clang
#      addons:
#        apt:
#          sources:
          #  - ubuntu-toolchain-r-test
          # the latest official clang on Xenial is clang-4.0 [https://packages.ubuntu.com/xenial/devel] => use llvm
#            - llvm-toolchain-xenial-7
          #  - llvm-toolchain-trusty-6.0
#          packages:
#            - clang-7
#      env:
#        - MATRIX_EVAL="ENV=Linux_clang-7_LLVM && CC=clang-7 && CXX=clang++-7 && clang --version"
      
#    - os: osx
#      osx_image: xcode10.2 # xcode9.2 (macOS 10.12) xcode10.2 (macOS 10.14)
#      compiler: clang
#      env:
#        - MATRIX_EVAL="ENV=Osx_clang-9.0_APPL && clang --version"
        #- 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: xcode10.2 #
#      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
        
before_install:
  - eval "${MATRIX_EVAL}"
  # Used to work without this 20190708. Now it stubbornly uses pre-installed older GCC.
  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
      sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-9 60 --slave /usr/bin/g++ g++ /usr/bin/g++-9 ;
      sudo update-alternatives --install /usr/bin/cpp cpp-bin /usr/bin/cpp-9 60 ;
    fi
  
install:
  # $HOME  /home/travis (Linux), /Users/travis (MacOS), /c/Users/travis (Windows)
  - pushd $HOME
  - env
  - echo $PWD
  - echo $PATH
  - which gcc-9
  - gcc-9 --version
  - gcc --version
  - echo $CC
  - echo $CXX
  # Python - Conda. Boot Conda using the existing Python 3
  - which pyenv
  - pyenv versions
  - python3 --version
  - pyenv global 3.7.1
  #- pyenv install –-list # errors for some reason. Travis bug.
  - which python3
  - python3 --version
  - which pip3
  - pip3 --version
  - pip3 install pyyaml
  - pip3 install jinja2
  - python3 $TRAVIS_BUILD_DIR/scripts/build.py --name conda
  - ls -lrt $HOME
  - export PATH="$HOME/miniconda3/bin:$PATH"
  - which pip
  - pip install numpy
  - pip install scipy
  - pip install scikit-bio

  - which cmake
  - cmake --version
  #
  # Upgrade CMake
  #
  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then 
      CMAKE_SH=cmake-${CMAKE_VER}-Linux-x86_64.sh ;
      wget ${CMAKE_URL}/v${CMAKE_VER}/${CMAKE_SH} ;
      sudo apt remove cmake ; 
      sudo apt purge --auto-remove cmake ;
    fi
  #- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
  #    brew upgrade cmake;
  #    brew install dos2unix;
  #  fi
  - python $TRAVIS_BUILD_DIR/scripts/build.py --name cmake
  - ls -lrt $HOME
  # add CMake to PATH
  - export PATH="$HOME/$(basename -- $(find $HOME -type d -name 'cmake-*x86_64'))/bin:$PATH"
  - echo $PATH
  - which cmake
  - cmake --version
  - popd

script:
  # check C++17 <filesystem>
  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
      find /usr/include -type f -name 'filesystem' ;
      find /usr/lib -type f -name '*fs.a' ;
    fi

  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
      ls -lrt /Applications ;
      find /Applications -type f -name 'filesystem' ;
      find /Applications -type f -name '*fs.a' ;
    fi

  # build SortmeRNA
  - python $TRAVIS_BUILD_DIR/scripts/build.py --name all

  # run tests
  #- export PATH="$PWD/dist/bin:$PATH"
  #- sortmerna --version
  #- sortmerna -h
  #- if [[ "$ENV" == "Linux+clang-7_LLVM" ]]; then python ./tests/test_sortmerna.py; fi
  #- if [[ "$ENV" == "Linux+gcc-7" ]]; then python ./tests/test_sortmerna_zlib.py; fi

#after_success:

before_deploy:
  - find ${TRAVIS_BUILD_DIR}/dist -type f
  - echo "Deploying SMR version [${TRAVIS_TAG:1}]"
  # add suffixes to installation files to indicate OS and linkage type
  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
      if [[ ${STATIC_LINK} == 1 ]]; then
        mv ${TRAVIS_BUILD_DIR}/dist/sortmerna-${TRAVIS_TAG:1}-Linux.sh ${TRAVIS_BUILD_DIR}/dist/sortmerna-${TRAVIS_TAG:1}-Linux-${OS_SFX}-static.sh ;
        mv ${TRAVIS_BUILD_DIR}/dist/sortmerna-${TRAVIS_TAG:1}-Linux.deb ${TRAVIS_BUILD_DIR}/dist/sortmerna-${TRAVIS_TAG:1}-Linux-${OS_SFX}-static.deb ;
      else
        mv ${TRAVIS_BUILD_DIR}/dist/sortmerna-${TRAVIS_TAG:1}-Linux.sh ${TRAVIS_BUILD_DIR}/dist/sortmerna-${TRAVIS_TAG:1}-Linux-${OS_SFX}.sh ;
        mv ${TRAVIS_BUILD_DIR}/dist/sortmerna-${TRAVIS_TAG:1}-Linux.deb ${TRAVIS_BUILD_DIR}/dist/sortmerna-${TRAVIS_TAG:1}-Linux-${OS_SFX}.deb ;
      fi
    fi
  #- echo "Get git tag"
  #- |
  #  xtag=$(git describe --exact-match HEAD 2>/dev/null); \
  #  if [[ ! -z "$xtag" ]]; then SMR_VER="${xtag:1}"; fi
  - echo "Deploying SMR version [${TRAVIS_TAG:1}]"
  - pwd
  - env

# This fails with "401 - Bad credentials // See: https://developer.github.com/v3 (Octokit::Unauthorized)"
# useless until the 'org' to 'com' migration is done.
#deploy:
#  provider: releases
#  api_key: "GITHUB OAUTH TOKEN"
#  file: 
#    - ${TRAVIS_BUILD_DIR}/dist/sortmerna-${TRAVIS_TAG:1}-Linux.sh
#    - ${TRAVIS_BUILD_DIR}/dist/sortmerna-${TRAVIS_TAG:1}-Linux.tar.gz
#  overwrite: true
#  skip_cleanup: true
#  on:
#    tags: true
#    condition: $ENV = "Linux+LLVM_clang-7"
## END .travis.yml