.travis.yml

# Language selection
# Note: with `language: cpp`, `cache: ccache` works
# but `cache: pip` and `python:` is ignored
language: cpp

# Currently commented out as set with environment flags
# Both clang and gcc can be tested. More is the better.
#compiler:
# - clang
# - gcc

# Environment variables
# Note: On trusty we need to build Armadillo and boost ourselves (the system versions are too old)
# Note: On OSX we can't test SYSTEM_Boost=OFF due to excessive log size (https://github.com/CCPPETMR/SIRF-SuperBuild/issues/167)
# Note: currently ACE is not building correctly, so ACE is not built on any configuration https://github.com/CCPPETMR/SIRF-SuperBuild/issues/#174
# Note: on Trusty, g++-7 causes errors with the system ACE, so cannot use g++-7 or later https://github.com/CCPPETMR/SIRF-SuperBuild/issues/169
# Note: altering the matrix here will cause re-building of caches,
# so try to keep this concise to avoid need to update
# Note: the line above each `env` contains a resume of the parameters passed to cmake.
#       + or - refer to the value of the parameter affecting the specific package is passed to cmake:
#       i.e. -boost == -DUSE_SYSTEM_Boost=OFF, which means that Boost will be built.
matrix:
 include:
 # linux g{cc,++}-6 py{27,3}
 - os: linux
   python: 3
   # -boost +fftw3 +hdf5 +ace
   env: EXTRA_BUILD_FLAGS="-DUSE_ITK:BOOL=ON -DUSE_SYSTEM_ITK:BOOL=ON -DUSE_SYSTEM_Boost=OFF -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON -DUSE_SYSTEM_ACE=ON" MATRIX_EVAL="CC=gcc-6 CXX=g++-6" PYMVER=3
 - os: linux
   python: 2.7
   # -boost +fftw3 +hdf5 +siemens_to_ismrmrd +swig +ace
   env: EXTRA_BUILD_FLAGS="-DUSE_ITK:BOOL=ON -DUSE_SYSTEM_ITK:BOOL=ON -DUSE_SYSTEM_Boost=OFF -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON -DBUILD_siemens_to_ismrmrd=ON -DUSE_SYSTEM_SWIG=ON -DUSE_SYSTEM_ACE=ON" MATRIX_EVAL="CC=gcc-6 CXX=g++-6" PYMVER=2
 - os: linux
   python: 3
   # +DEVEL -boost -hdf5 -fftw3 +ace +siemens_to_ismrmrd
   env: EXTRA_BUILD_FLAGS="-DDEVEL_BUILD=ON -DUSE_SYSTEM_Boost=OFF -DUSE_SYSTEM_HDF5=OFF -DUSE_SYSTEM_FFTW3=OFF -DUSE_SYSTEM_ACE=ON -DBUILD_siemens_to_ismrmrd=ON" MATRIX_EVAL="CC=gcc-6 CXX=g++-6" PYMVER=3
 - os: linux
   python: 2.7
   # +DEVEL -boost -fftw3 -hdf5 -swig +ace
   env: EXTRA_BUILD_FLAGS="-DUSE_ITK:BOOL=ON -DUSE_SYSTEM_ITK:BOOL=ON -DDEVEL_BUILD=ON -DUSE_SYSTEM_Boost=OFF -DUSE_SYSTEM_FFTW3=OFF -DUSE_SYSTEM_HDF5=ON -DUSE_SYSTEM_ACE=ON -DUSE_SYSTEM_SWIG=OFF" MATRIX_EVAL="CC=gcc-6 CXX=g++-6" PYMVER=2
 # osx g{cc,++} py{27,36}
 - os: osx
   osx_image: xcode11.2
   python: 2.7
   # +boost -hdf5 -swig
   env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_HDF5=OFF -DUSE_SYSTEM_SWIG=OFF" MATRIX_EVAL="CC=gcc CXX=g++" PYMVER=2
 - os: osx
   # +boost +fftw3 -hdf5 -swig
   osx_image: xcode11.2
   python: 3
   env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=OFF -DUSE_SYSTEM_SWIG=OFF" MATRIX_EVAL="CC=gcc CXX=g++" PYMVER=3
 - os: osx
   python: 2.7
   # +DEVEL +boost -hdf5 +swig
   osx_image: xcode11.2
   env: EXTRA_BUILD_FLAGS="-DDEVEL_BUILD=ON -DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_HDF5=OFF -DUSE_SYSTEM_SWIG=ON" MATRIX_EVAL="CC=gcc CXX=g++" PYMVER=2
 - os: osx
   python: 2.7
   # +DEVEL +boost -fftw3 -hdf5 +swig +itk
   osx_image: xcode11.2
   env: EXTRA_BUILD_FLAGS="-DDEVEL_BUILD=ON -DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_FFTW3=OFF -DUSE_SYSTEM_HDF5=OFF -DUSE_SYSTEM_SWIG=ON -DUSE_ITK=ON" MATRIX_EVAL="CC=gcc CXX=g++" PYMVER=2
 - os: linux
   python: 3
   # -boost +itk +fftw3 +hdf5
   env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=OFF -DUSE_ITK=ON -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON" MATRIX_EVAL="CC=gcc-6 CXX=g++-6" PYMVER=3
 - os: osx
   python: 2.7
   # +boost +itk -hdf5 +swig
   osx_image: xcode11.2
   env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=ON -DUSE_ITK=ON -DUSE_SYSTEM_HDF5=OFF -DUSE_SYSTEM_SWIG=ON" MATRIX_EVAL="CC=gcc CXX=g++" PYMVER=2

env:
 global:
  # Need STIR_TAG=master at present, see https://github.com/CCPPETMR/SIRF/issues/366
  - BUILD_FLAGS="-DCMAKE_BUILD_TYPE=Release -DSTIR_TAG=master"
  # don't use too many threads - may crash
  - MAKEFLAGS="-j 2"

# Ubuntu 14.04 LTS
dist: xenial

# No need for sudo
sudo: false

# Compilation dependencies
addons:
 apt:
  sources:
   - ubuntu-toolchain-r-test
  packages:
   - git-core
   - build-essential
   - g++-6
   - g++-7
   - libboost-all-dev
   - libhdf5-serial-dev
   - libfftw3-dev
   - python-dev
   - python3-dev
   - python-tk
   - python3-tk
   - libopenblas-dev
   - libatlas-base-dev
   - liblapack-dev
   - libxml2-dev
   - libarmadillo-dev
   - libgtest-dev
   - libplplot-dev
   - swig
   - ccache
   # not in whitelist
   - libxslt-dev
   - libace-dev
   # - root-system-bin
   - libinsighttoolkit4-dev

# cache C/C++/pip
cache:
 - ccache
 - pip

before_install:
 # Set C and C++ compiler etc using trick from
 # https://docs.travis-ci.com/user/languages/cpp/#c11c11-and-beyond-and-toolchain-versioning
 - eval "${MATRIX_EVAL}"
 - $CC --version
 - $CXX --version
 - mkdir -p ~/.local/bin
 - pushd ~/.local/bin
 # Note: use ( set -ev; ... ) to echo commands and exit immediately on failure
 # in compounds statements (note that export/cd etc won't persist).
 - |
    if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
      brew update
      BUILD_FLAGS="$BUILD_FLAGS -DSHARED_LIBS_ABS_PATH=ON"
      brew install openblas
      # Get openblas version
      blas_ver=$(brew list --versions openblas)
      blas_ver=${blas_ver#"openblas "}
      EXTRA_BUILD_FLAGS="$EXTRA_BUILD_FLAGS -DCBLAS_INCLUDE_DIR=/usr/local/Cellar/openblas/${blas_ver}/include -DCBLAS_LIBRARY=/usr/local/Cellar/openblas/${blas_ver}/lib/libblas.dylib"
      if [ $PYMVER == 2 ]; then
        PYINST=/System/Library/Frameworks/Python.framework/Versions/$PYMVER.7
        PY_EXE=$PYINST/bin/python2.7
        # Next lines are not necessary if we give the actual path for the executable to cmake
        #BUILD_FLAGS="$BUILD_FLAGS -DPYTHON_LIBRARY=$PYINST/lib/libpython2.7.dylib"
        #BUILD_FLAGS="$BUILD_FLAGS -DPYTHON_INCLUDE_DIR=$PYINST/include/python2.7"
      else
        brew upgrade python || true # don't fail if upgrading doesn't do anything
        # find exact location of Python executable to pass to CMake
        # we attempt to find the last one if there are multiple Python 3 versions installed
        PY_INST=$(ls -d1 /usr/local/Cellar/python/$PYMVER.*/Frameworks/Python.framework/Versions/$PYMVER.*|tail -n 1)
        PYMVER=$(basename ${PY_INST})
        PY_EXE=$PY_INST/bin/python$PYMVER
        if [ ! -x "$PY_EXE" ]; then
          echo "Something wrong with finding Python executable for OSX"
          echo "PY_EXE = $PY_EXE"
          travis_terminate 1
        fi
        # Next lines are not necessary if we give the actual path for the executable to cmake
        #PY_LIB=$PY_INST/Python
        #PY_INC=$PY_INST/Headers
        # BUILD_FLAGS="$BUILD_FLAGS -DPYTHON_LIBRARY=$PY_LIB -DPYTHON_INCLUDE_DIR=$PY_INC"
      fi
      BUILD_FLAGS="$BUILD_FLAGS -DPYTHON_EXECUTABLE=$PY_EXE"
      ( set -ev
        # boost is already installed but 1.65 doesn't work so update
        brew reinstall boost
        # we currently need boost-python
        # brew install boost-python
        brew install ace
        brew install swig
        brew install ccache
        if [[ $EXTRA_BUILD_FLAGS == *"SYSTEM_FFTW3=ON"* ]]; then
            brew install fftw
        else
            echo "Not installing FFTW as we are building it"
        fi
        # need curl to get pip and more recent cmake
        brew install curl
        #brew install cmake # already present
        # alternative: get our own
        #curl -L -O https://cmake.org/files/v3.8/cmake-3.8.0-Darwin-x86_64.tar.gz
        #tar xzf cmake-*.tar.gz
        #mv cmake-*/CMake.app/Contents/* cmake
        #export PATH="$PWD/cmake/bin:$PATH"
      )
    elif [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
      PY_EXE=python$PYMVER
      curl -L -O https://github.com/Kitware/CMake/releases/download/v3.13.1/cmake-3.13.1-Linux-x86_64.tar.gz
      ls -l cmake-*
      tar xzf cmake-*.tar.gz
      mv cmake-*x86_64 cmake
      export PATH="$PWD/cmake/bin:$PATH"
    fi
 - echo "Using Python executable $PY_EXE"
 # get pip
 - curl -0 https://bootstrap.pypa.io/get-pip.py -o get-pip.py
 - $PY_EXE get-pip.py --user
 # setuptools may be out of date on osx
 - $PY_EXE -m pip install --user -U pip setuptools wheel
 # ensure python bin dir exists (and coverage dependencies installed)
 - $PY_EXE -m pip install --user -U nose codecov coveralls requests deprecation
 # for counting clones, excluding ours
 - |
    if [[ -n "$GITHUB_API_TOKEN" ]]; then
      git clone https://$GITHUB_API_TOKEN@github.com/ccp-petmr-codebot/github-stats --branch CCPPETMR/SIRF-SuperBuild
      # update with last fortnight's clones from GitHub API
      TRAVIS_REPO_SLUG=CCPPETMR/SIRF-SuperBuild source github-stats/setup.sh
      # count unique clones, excluding travis, and print total
      TRAVIS_REPO_SLUG=CCPPETMR/SIRF-SuperBuild gh_stats_count -k uniques
    fi
 - $PY_EXE --version
 - $PY_EXE -m pip --version
 - $PY_EXE -m pip freeze
 # ccache compiler override
 - ln -s "$(which ccache)" g++
 - ln -s "$(which ccache)" g++-6
 - ln -s "$(which ccache)" g++-7

 - ln -s "$(which ccache)" gcc
 - ln -s "$(which ccache)" gcc-6
 - ln -s "$(which ccache)" gcc-7

 - export PATH="$PWD:$PATH"
 - popd
 # ensure a branch exists (for e.g. PRs)
 - git symbolic-ref -q HEAD || git checkout -b local_$TRAVIS_COMMIT
 # Use Travis' currently checked-out SIRF commit ID to build.
 # Also no point re-downloading SIRF - just use local URL.
 # N.B.: don't put into build matrix to allow caching.
 - BUILD_FLAGS="$BUILD_FLAGS -DPYVER=$PYMVER -DSIRF_URL=$PWD -DSIRF_TAG=$TRAVIS_COMMIT"
 # get SuperBuild
 - cd ..
 - git clone https://github.com/CCPPETMR/SIRF-SuperBuild --recursive -b master
 - cd SIRF-SuperBuild
 - cmake --version

install:
 - $PY_EXE -m pip install --user --only-binary=numpy,scipy,matplotlib numpy scipy matplotlib nibabel
 - cmake $BUILD_FLAGS $EXTRA_BUILD_FLAGS .
 # Job may timeout (>50min) if no ccache, otherwise should be <1min:
 - make
 - mv INSTALL/share/gadgetron/config/gadgetron.xml.example INSTALL/share/gadgetron/config/gadgetron.xml
 - source $PWD/INSTALL/bin/env_ccppetmr.sh

script:
 - ./INSTALL/bin/gadgetron >& gadgetron.log&
 # print for debugging
 - cat builds/SIRF/build/CMakeCache.txt
 - ctest -VV
 # print for debugging
 - cat builds/SIRF/build/Testing/Temporary/LastTest.log
 - echo "----------- Last 200 lines of gadgetron.log"
 - tail -n 200 gadgetron.log

after_success:
 - pushd ../SIRF
 - sed -r 's/SIRF-SuperBuild\/INSTALL\/python\/sirf\/(\w*)\.py/SIRF\/src\/x\1\/p\1\/\1.py/g' ../SIRF-SuperBuild/sources/SIRF/.coverage > .coverage
 - codecov
 - coveralls
 - popd